Query         gi|254780885|ref|YP_003065298.1| hypothetical protein CLIBASIA_03910 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 207
No_of_seqs    61 out of 63
Neff          4.3 
Searched_HMMs 39220
Date          Tue May 31 15:24:54 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780885.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam07238 PilZ PilZ domain. Th  98.3 2.2E-05 5.6E-10   53.3  11.4   87   13-100     2-97  (102)
  2 pfam07238 PilZ PilZ domain. Th  98.3 5.6E-06 1.4E-10   56.9   8.2   86  116-206     1-100 (102)
  3 PRK11498 bcsA cellulose syntha  98.1   9E-05 2.3E-09   49.5  11.6   93    9-102   691-788 (858)
  4 PRK11498 bcsA cellulose syntha  97.6 0.00071 1.8E-08   44.0   8.7   75  115-192   693-777 (858)
  5 TIGR03030 CelA cellulose synth  97.5  0.0012 3.1E-08   42.6   8.8   93   10-103   566-667 (713)
  6 TIGR03030 CelA cellulose synth  97.4  0.0061 1.6E-07   38.3  11.9   79  114-195   566-658 (713)
  7 COG5581 c-di-GMP-binding prote  95.6     0.2 5.1E-06   29.1  10.0  171   27-207    24-220 (233)
  8 COG5581 c-di-GMP-binding prote  95.4    0.24   6E-06   28.6   9.3  102    6-108   103-224 (233)
  9 cd07705 Ig2_Necl-1 Second immu  85.2    0.29 7.4E-06   28.1   0.5   66   98-163    12-82  (83)
 10 PRK11642 exoribonuclease R; Pr  83.7     3.7 9.4E-05   21.3   6.3   74    7-82     58-147 (813)
 11 TIGR02266 gmx_TIGR02266 Myxoco  83.6     1.2 3.2E-05   24.2   3.2   62  133-194     7-86  (97)
 12 cd05885 Ig2_Necl-4 Second immu  74.7    0.64 1.6E-05   26.0  -0.6   64   97-163    11-79  (80)
 13 cd05884 Ig2_Necl-3 Second immu  71.6     1.2 2.9E-05   24.4   0.1   59   97-155    11-74  (83)
 14 COG0179 MhpD 2-keto-4-pentenoa  52.3      19 0.00048   16.9   3.6   14   84-97    140-153 (266)
 15 cd05761 Ig2_Necl-1-4_like Seco  52.0     3.2 8.1E-05   21.7  -0.6   61   98-162    12-80  (82)
 16 TIGR02305 HpaG-N-term 4-hydrox  49.4      16  0.0004   17.5   2.6   35   42-76    169-206 (206)
 17 pfam08205 C2-set_2 CD80-like C  45.3     7.1 0.00018   19.6   0.4   56   98-153    27-87  (89)
 18 TIGR00037 eIF_5A translation i  45.0       8  0.0002   19.2   0.6   10   35-44     23-32  (137)
 19 TIGR02303 HpaG-C-term 4-hydrox  43.9      26 0.00066   16.1   3.4   42   35-77    202-247 (249)
 20 COG0809 QueA S-adenosylmethion  43.4      26 0.00067   16.1   7.6   35  157-191    97-133 (348)
 21 KOG1989 consensus               41.0      29 0.00073   15.9   4.7   28   69-96     34-61  (738)
 22 KOG3591 consensus               40.8      29 0.00073   15.8   5.1   79   80-164    69-151 (173)
 23 PRK13613 lipoprotein LpqB; Pro  40.3     8.6 0.00022   19.0   0.2   20   90-109   268-287 (603)
 24 cd05759 Ig2_KIRREL3-like Secon  39.7     6.3 0.00016   19.9  -0.6   53   98-152    12-71  (82)
 25 cd05883 Ig2_Necl-2 Second immu  37.9     8.3 0.00021   19.2  -0.2   54   97-152    11-69  (82)
 26 cd06475 ACD_HspB1_like Alpha c  37.6      31 0.00078   15.7   2.6   30   22-51     54-83  (86)
 27 cd06479 ACD_HspB7_like Alpha c  33.1      38 0.00097   15.1   3.2   29   23-51     50-78  (81)
 28 cd06476 ACD_HspB2_like Alpha c  32.6      38 0.00098   15.1   2.5   33   19-51     48-80  (83)
 29 TIGR02037 degP_htrA_DO proteas  32.5      39 0.00099   15.0   2.7   15  133-147   118-132 (484)
 30 cd05696 S1_Rrp5_repeat_hs4 S1_  31.0      34 0.00085   15.4   2.0   18  135-152    46-63  (71)
 31 PRK10929 hypothetical protein;  30.1      25 0.00063   16.3   1.2   29  152-180   926-954 (1109)
 32 PRK11281 potassium efflux prot  29.1      26 0.00066   16.1   1.1   29  152-180   928-956 (1107)
 33 cd05853 Ig6_Contactin-4 Sixth   29.0      20 0.00052   16.8   0.6   45  103-147    19-67  (85)
 34 pfam10128 OpcA_G6PD_assem Gluc  28.9      34 0.00085   15.4   1.7   12   33-44      7-18  (267)
 35 cd05854 Ig6_Contactin-2 Sixth   28.3      16 0.00041   17.4  -0.0   46  103-148    19-68  (85)
 36 cd06480 ACD_HspB8_like Alpha-c  27.3      48  0.0012   14.5   3.9   33   19-51     56-88  (91)
 37 PTZ00328 eukaryotic initiation  26.5      35 0.00089   15.3   1.4   73   20-96     27-119 (166)
 38 pfam11356 Pilus_PilP Type IV p  23.9      56  0.0014   14.1   3.3   25  146-170    60-84  (108)
 39 cd04970 Ig6_Contactin_like Six  23.6      24 0.00062   16.3   0.2   46  103-148    19-68  (85)
 40 cd03079 GST_N_Metaxin2 GST_N f  23.4      31 0.00079   15.7   0.7   27   39-70     42-68  (74)
 41 PRK13616 lipoprotein LpqB; Pro  22.4      44  0.0011   14.7   1.3   26   85-110   250-279 (590)
 42 cd06497 ACD_alphaA-crystallin_  22.0      60  0.0015   13.9   2.6   33   19-51     51-83  (86)
 43 pfam01356 A_amylase_inhib Alph  20.5      65  0.0017   13.7   2.5   18  130-147    27-44  (68)
 44 cd04979 Ig_Semaphorin_C Immuno  20.4      18 0.00045   17.1  -1.1   46  100-146    24-70  (89)
 45 cd07703 Ig2_Nectin-2_like Seco  20.1      50  0.0013   14.4   1.2   52   97-151    27-83  (95)
 46 smart00783 A_amylase_inhib Alp  20.1      66  0.0017   13.6   2.5   18  130-147    28-45  (69)

No 1  
>pfam07238 PilZ PilZ domain. This domain is found in a wide variety of bacterial signalling proteins.
Probab=98.28  E-value=2.2e-05  Score=53.27  Aligned_cols=87  Identities=29%  Similarity=0.440  Sum_probs=36.6

Q ss_pred             HCCCEEEEEEEEEEEEECCCCCEEEEEEEECCCCEEEEECCCCCCCCCEEEE--EECCCCC---EEEEEEEECCCC---C
Q ss_conf             1062147999705799468983026999875685499942788767974999--9955443---769999930898---3
Q gi|254780885|r   13 QRAFQRVKVDLKGRFLLFDGTEYNCIVREISPGGLCIVCDVPMFLVGERSIV--FVEKVGR---IEGKVVNFDSNR---G   84 (207)
Q Consensus        13 rR~f~RV~v~l~GR~ll~d~~E~~C~t~diSpgg~~l~~~~~~~~~Gervv~--Yld~iGr---lEG~V~r~~~~~---G   84 (207)
                      +|.+.|+++.++......+..++.|.+.|+|.||+++..+.+ ...|+.+.+  ++...+.   +.|+|++.....   .
T Consensus         2 rR~~~R~~~~~~~~~~~~~~~~~~~~~~DiS~gG~~i~~~~~-~~~g~~v~~~~~~~~~~~~~~~~~~Vv~~~~~~~~~~   80 (102)
T pfam07238         2 RRREPRVPVNLPVTLLLGGGELYSGVIIDISLGGAALRLPEP-LQLGDEVRLRLTLPDDGIKLLVPGRVVRIRPDGDGYG   80 (102)
T ss_pred             CCCCCEECEEEEEEEECCCCCEEEEEEHHHCCCCEEEECCCC-CCCCCEEEEEEEECCCCEEEEEEEEEEEECCCCCCEE
T ss_conf             678745035788999938998999996443788489970876-5579719999996999808982789999915898289


Q ss_pred             EEEEE-ECCHHHHHHHH
Q ss_conf             89999-76987899999
Q gi|254780885|r   85 YAVRI-VTSENERRKLA  100 (207)
Q Consensus        85 Fav~l-~~t~~kR~kLA  100 (207)
                      +.++| +.+....+.|.
T Consensus        81 ~G~~F~~~~~~~~~~l~   97 (102)
T pfam07238        81 VGVQFLELDEESRRLLE   97 (102)
T ss_pred             EEEEEEECCHHHHHHHH
T ss_conf             98899539999999879


No 2  
>pfam07238 PilZ PilZ domain. This domain is found in a wide variety of bacterial signalling proteins.
Probab=98.27  E-value=5.6e-06  Score=56.90  Aligned_cols=86  Identities=24%  Similarity=0.287  Sum_probs=65.8

Q ss_pred             HHCCCCCCCCCCCCCEEEEEECCCCEEEEEEEEEECCCEEEECCCCCCCCCEEEE-------CC---EEEEEEEEECC--
Q ss_conf             2102567477776513689957998898999987424204551577899855897-------34---66999999389--
Q gi|254780885|r  116 DCRAYGRKITRDREVDAQLVLNDNTKHSCKVIDISESGVSVSVDLQIEMFSKVLF-------ND---ILGRVVRIFPG--  183 (207)
Q Consensus       116 e~R~h~R~vPr~~~~~~~l~l~DG~~~~criiDiS~SGAAi~~~~rp~iGs~V~v-------G~---~~grVVRh~~~--  183 (207)
                      +.|.+.|+....+.   .....++..+.|.++|+|.+|+++..+..+++|+.|.+       +.   +.|+||+.-.+  
T Consensus         1 ~rR~~~R~~~~~~~---~~~~~~~~~~~~~~~DiS~gG~~i~~~~~~~~g~~v~~~~~~~~~~~~~~~~~~Vv~~~~~~~   77 (102)
T pfam07238         1 QRRREPRVPVNLPV---TLLLGGGELYSGVIIDISLGGAALRLPEPLQLGDEVRLRLTLPDDGIKLLVPGRVVRIRPDGD   77 (102)
T ss_pred             CCCCCCEECEEEEE---EEECCCCCEEEEEEHHHCCCCEEEECCCCCCCCCEEEEEEEECCCCEEEEEEEEEEEECCCCC
T ss_conf             96787450357889---999389989999964437884899708765579719999996999808982789999915898


Q ss_pred             --EEEEEECCCCCCCHHHHHHHHHC
Q ss_conf             --08999716778423677875303
Q gi|254780885|r  184 --GIAIEFSSVQESNIAFKSLINHC  206 (207)
Q Consensus       184 --GfaVeF~~~q~~~~~~~~~~~~~  206 (207)
                        .+|++|.++.  +.....+.+++
T Consensus        78 ~~~~G~~F~~~~--~~~~~~l~~~~  100 (102)
T pfam07238        78 GYGVGVQFLELD--EESRRLLERLL  100 (102)
T ss_pred             CEEEEEEEEECC--HHHHHHHHHHH
T ss_conf             289988995399--99999879862


No 3  
>PRK11498 bcsA cellulose synthase catalytic subunit; Provisional
Probab=98.11  E-value=9e-05  Score=49.53  Aligned_cols=93  Identities=17%  Similarity=0.295  Sum_probs=71.3

Q ss_pred             HHHHHCCCEEEEEEEEEEEEECCCCCEEEEEEEECCCCEEEEECCCCC-CCCCEEEEEECCCCC---EEEEEEEECCCCC
Q ss_conf             222010621479997057994689830269998756854999427887-679749999955443---7699999308983
Q gi|254780885|r    9 QFIDQRAFQRVKVDLKGRFLLFDGTEYNCIVREISPGGLCIVCDVPMF-LVGERSIVFVEKVGR---IEGKVVNFDSNRG   84 (207)
Q Consensus         9 ~~~drR~f~RV~v~l~GR~ll~d~~E~~C~t~diSpgg~~l~~~~~~~-~~Gervv~Yld~iGr---lEG~V~r~~~~~G   84 (207)
                      ...+-|++.||++++++...++|+..++|++.|.|-||+.+..+.+.. ..|+.+.+.+..-++   +.++|++...+ -
T Consensus       691 E~rQvR~~hRv~~~~pa~l~~~dG~~~~c~~~d~S~gG~gl~l~~~~~~~~~~~v~v~l~rg~~~~~fp~~v~~~~~~-~  769 (858)
T PRK11498        691 ESKQVRRSHRVEMTMPAAIAREDGHLFSCTVQDFSDGGLGIKINGQAQLLEGQKVNLLLKRGQQEYVFPTQVTRVMGN-E  769 (858)
T ss_pred             HHHHHHCCCCEEECCCEEEEECCCCEEEEEEEEECCCCEEEEECCCCCCCCCCEEEEEEECCCEEEEEEEEEEEECCC-E
T ss_conf             887653146235505249990798789889987037851586078765799984899994298867501699983397-6


Q ss_pred             EEEEEE-CCHHHHHHHHHH
Q ss_conf             899997-698789999999
Q gi|254780885|r   85 YAVRIV-TSENERRKLADK  102 (207)
Q Consensus        85 Fav~l~-~t~~kR~kLA~q  102 (207)
                      ..+++. .|.++...+..+
T Consensus       770 ~gl~~~~lt~~q~~~~vqc  788 (858)
T PRK11498        770 VGLQLMPLTTQQHIDFVQC  788 (858)
T ss_pred             EEEEECCCCHHHHHHHHHH
T ss_conf             7897366899999988965


No 4  
>PRK11498 bcsA cellulose synthase catalytic subunit; Provisional
Probab=97.56  E-value=0.00071  Score=44.03  Aligned_cols=75  Identities=20%  Similarity=0.303  Sum_probs=61.6

Q ss_pred             CHHCCCCCCCCCCCCCEEEEEECCCCEEEEEEEEEECCCEEEECCCC--CCCCCEEEE----CC----EEEEEEEEECCE
Q ss_conf             02102567477776513689957998898999987424204551577--899855897----34----669999993890
Q gi|254780885|r  115 QDCRAYGRKITRDREVDAQLVLNDNTKHSCKVIDISESGVSVSVDLQ--IEMFSKVLF----ND----ILGRVVRIFPGG  184 (207)
Q Consensus       115 ~e~R~h~R~vPr~~~~~~~l~l~DG~~~~criiDiS~SGAAi~~~~r--p~iGs~V~v----G~----~~grVVRh~~~G  184 (207)
                      ...|++.|+.-+-|   +.+.++||..++|.++|.|..|+.+..+..  .+.|..|++    |.    .+++|+|..++-
T Consensus       693 rQvR~~hRv~~~~p---a~l~~~dG~~~~c~~~d~S~gG~gl~l~~~~~~~~~~~v~v~l~rg~~~~~fp~~v~~~~~~~  769 (858)
T PRK11498        693 KQVRRSHRVEMTMP---AAIAREDGHLFSCTVQDFSDGGLGIKINGQAQLLEGQKVNLLLKRGQQEYVFPTQVTRVMGNE  769 (858)
T ss_pred             HHHHCCCCEEECCC---EEEEECCCCEEEEEEEEECCCCEEEEECCCCCCCCCCEEEEEEECCCEEEEEEEEEEEECCCE
T ss_conf             76531462355052---499907987898899870378515860787657999848999942988675016999833976


Q ss_pred             EEEEECCC
Q ss_conf             89997167
Q gi|254780885|r  185 IAIEFSSV  192 (207)
Q Consensus       185 faVeF~~~  192 (207)
                      +|++|...
T Consensus       770 ~gl~~~~l  777 (858)
T PRK11498        770 VGLQLMPL  777 (858)
T ss_pred             EEEEECCC
T ss_conf             78973668


No 5  
>TIGR03030 CelA cellulose synthase catalytic subunit (UDP-forming). Cellulose synthase catalyzes the beta-1,4 polymerization of glucose residues in the formation of cellulose. In bacteria, the substrate is UDP-glucose. The synthase consists of two subunits (or domains in the frequent cases where it is encoded as a single polypeptide), the catalytic domain modelled here and the regulatory domain (pfam03170). The regulatory domain binds the allosteric activator cyclic di-GMP. The protein is membrane-associated and probably assembles into multimers such that the individual cellulose strands can self-assemble into multi-strand fibrils.
Probab=97.46  E-value=0.0012  Score=42.58  Aligned_cols=93  Identities=15%  Similarity=0.137  Sum_probs=53.1

Q ss_pred             HHHHCCCEEEEEEEEEEEEECCCCCEEEEEEEECCCCEEEEECCC-----CCCCCCEEEEEECCCCC---EEEEEEEECC
Q ss_conf             220106214799970579946898302699987568549994278-----87679749999955443---7699999308
Q gi|254780885|r   10 FIDQRAFQRVKVDLKGRFLLFDGTEYNCIVREISPGGLCIVCDVP-----MFLVGERSIVFVEKVGR---IEGKVVNFDS   81 (207)
Q Consensus        10 ~~drR~f~RV~v~l~GR~ll~d~~E~~C~t~diSpgg~~l~~~~~-----~~~~Gervv~Yld~iGr---lEG~V~r~~~   81 (207)
                      .-++|+..|++++.+++..++|+..++|.|.|+|.||+.+.-+..     ....|+.+..-+..-+.   +..+|.+.. 
T Consensus       566 ~~q~R~~~R~~~~~~~~l~~~~g~~~~~~t~D~S~gG~~i~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~v~~~~-  644 (713)
T TIGR03030       566 RRQRRSSPRIPCKIPAEVQRDGGRWVEATVEDASVGGLGIKINAQGAPGPQLGAGVLVQIRPKRNGLPALKPARVRGAG-  644 (713)
T ss_pred             CCCCCCCCCEEECCEEEEEECCCCEEEEEEEECCCCCEEEEECCCCCCCCCCCCCCEEEEEECCCCEEEEEEEEEEECC-
T ss_conf             5544656615613249999789978999998816786179845776766567888339999657981678779999558-


Q ss_pred             CCCEEEEEE-CCHHHHHHHHHHH
Q ss_conf             983899997-6987899999999
Q gi|254780885|r   82 NRGYAVRIV-TSENERRKLADKL  103 (207)
Q Consensus        82 ~~GFav~l~-~t~~kR~kLA~qL  103 (207)
                      +....+.+. .|.++..++++.+
T Consensus       645 ~~~~~l~f~~~~~~~~~~lv~~~  667 (713)
T TIGR03030       645 GVMIGLEFSPLNVQQVREIVDLV  667 (713)
T ss_pred             CCEEEEEEECCCHHHHHHHHHHH
T ss_conf             97799998159989999999980


No 6  
>TIGR03030 CelA cellulose synthase catalytic subunit (UDP-forming). Cellulose synthase catalyzes the beta-1,4 polymerization of glucose residues in the formation of cellulose. In bacteria, the substrate is UDP-glucose. The synthase consists of two subunits (or domains in the frequent cases where it is encoded as a single polypeptide), the catalytic domain modelled here and the regulatory domain (pfam03170). The regulatory domain binds the allosteric activator cyclic di-GMP. The protein is membrane-associated and probably assembles into multimers such that the individual cellulose strands can self-assemble into multi-strand fibrils.
Probab=97.42  E-value=0.0061  Score=38.32  Aligned_cols=79  Identities=20%  Similarity=0.123  Sum_probs=57.0

Q ss_pred             CCHHCCCCCCCCCCCCCEEEEEECCCCEEEEEEEEEECCCEEEECC------CCCCCCCEEEE----CC----EEEEEEE
Q ss_conf             5021025674777765136899579988989999874242045515------77899855897----34----6699999
Q gi|254780885|r  114 LQDCRAYGRKITRDREVDAQLVLNDNTKHSCKVIDISESGVSVSVD------LQIEMFSKVLF----ND----ILGRVVR  179 (207)
Q Consensus       114 l~e~R~h~R~vPr~~~~~~~l~l~DG~~~~criiDiS~SGAAi~~~------~rp~iGs~V~v----G~----~~grVVR  179 (207)
                      -+..|.++|+.-+.|   +.+.++||..++|.+.|+|..|+.+..+      ..+..+..+.+    |+    ..++|++
T Consensus       566 ~~q~R~~~R~~~~~~---~~l~~~~g~~~~~~t~D~S~gG~~i~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~v~~  642 (713)
T TIGR03030       566 RRQRRSSPRIPCKIP---AEVQRDGGRWVEATVEDASVGGLGIKINAQGAPGPQLGAGVLVQIRPKRNGLPALKPARVRG  642 (713)
T ss_pred             CCCCCCCCCEEECCE---EEEEECCCCEEEEEEEECCCCCEEEEECCCCCCCCCCCCCCEEEEEECCCCEEEEEEEEEEE
T ss_conf             554465661561324---99997899789999988167861798457767665678883399996579816787799995


Q ss_pred             EECCEEEEEECCCCCC
Q ss_conf             9389089997167784
Q gi|254780885|r  180 IFPGGIAIEFSSVQES  195 (207)
Q Consensus       180 h~~~GfaVeF~~~q~~  195 (207)
                      -.+.-++++|......
T Consensus       643 ~~~~~~~l~f~~~~~~  658 (713)
T TIGR03030       643 AGGVMIGLEFSPLNVQ  658 (713)
T ss_pred             CCCCEEEEEEECCCHH
T ss_conf             5897799998159989


No 7  
>COG5581 c-di-GMP-binding protein [Signal transduction mechanisms]
Probab=95.60  E-value=0.2  Score=29.06  Aligned_cols=171  Identities=19%  Similarity=0.196  Sum_probs=91.8

Q ss_pred             EEECCCCC-EEEEEEEECCCCEEEEECCCCCCCCCEEEEEECCCCCEEEEEEEECCCCCEEEEEECCHHHHHHHHHHHHH
Q ss_conf             99468983-02699987568549994278876797499999554437699999308983899997698789999999998
Q gi|254780885|r   27 FLLFDGTE-YNCIVREISPGGLCIVCDVPMFLVGERSIVFVEKVGRIEGKVVNFDSNRGYAVRIVTSENERRKLADKLIW  105 (207)
Q Consensus        27 ~ll~d~~E-~~C~t~diSpgg~~l~~~~~~~~~Gervv~Yld~iGrlEG~V~r~~~~~GFav~l~~t~~kR~kLA~qLtW  105 (207)
                      +++++... |.|...|+.|....+.-|.+. ..|+-+++.=..  .+.-.+  ...+.=+.++.+.-.+++|++.--..|
T Consensus        24 ~~~~~~~~q~~S~ivdI~~e~~~ia~d~~~-~~~~~~~l~~g~--~~ti~~--~~~~a~y~Fts~~l~~~~e~~~lp~f~   98 (233)
T COG5581          24 VRLENAGGQYKSKIVDIDPEEGVIALDFGS-QNGRNVILLKGT--QFTIEA--EHKGAKYEFTSEVLEQVKEYLQLPAFS   98 (233)
T ss_pred             EEECCCCCEEEEEEEEECCCCCEEEEECCC-CCCCEEEECCCC--EEEEEE--ECCCCEEEEEEEEHCCCCCCCCCEEEC
T ss_conf             775234631454456205666679863266-568566512895--599999--548957999983110023511540672


Q ss_pred             HHCCCCCCCCHHCCCCC----CCCCCCCCEEEEEECCCCEEEEEEEEEECCCEEEECCCC--CCCCCEEEE-------C-
Q ss_conf             76424367502102567----477776513689957998898999987424204551577--899855897-------3-
Q gi|254780885|r  106 LANKDDLHLQDCRAYGR----KITRDREVDAQLVLNDNTKHSCKVIDISESGVSVSVDLQ--IEMFSKVLF-------N-  171 (207)
Q Consensus       106 lanr~~l~l~e~R~h~R----~vPr~~~~~~~l~l~DG~~~~criiDiS~SGAAi~~~~r--p~iGs~V~v-------G-  171 (207)
                      -.-...+-.=.+|..=|    .-|.-.   ..-++.|+..+-....|+|+.|.++-.+.-  ++++....+       + 
T Consensus        99 ~p~pe~lkriQRR~~fRvsa~l~~~y~---~~~~~~d~~~lr~~~~DiS~GGm~~vl~~gl~~~l~e~~~~~~~~~~~~~  175 (233)
T COG5581          99 TPPPETLKRIQRRRYFRVSAPLSPPYY---VQNKLTDEEPLRFTLYDISAGGMGLVLEGGLSFRLHEGIRYVDALVDEGQ  175 (233)
T ss_pred             CCCHHHHHHHHHHHHEEECCCCCCCEE---ECCCCCCCCCCEEEEEEECCCCHHEEECCCCCCCCCCCCEEEEEECCCCC
T ss_conf             599799889887664563420146455---32566765651237886047632011077767576787378764010565


Q ss_pred             -----CEEEEEEEEE------CCEEEEEECCCCCCCHHHHHHHHHCC
Q ss_conf             -----4669999993------89089997167784236778753039
Q gi|254780885|r  172 -----DILGRVVRIF------PGGIAIEFSSVQESNIAFKSLINHCY  207 (207)
Q Consensus       172 -----~~~grVVRh~------~~GfaVeF~~~q~~~~~~~~~~~~~~  207 (207)
                           ...++|||.+      +--.++||++  =+...++++++-||
T Consensus       176 d~~li~~~~~vv~~~k~e~~~~~r~~leFl~--is~~~er~l~r~~F  220 (233)
T COG5581         176 DQQLISISARVVRIRKDEKLGERRLGLEFLE--ISPRIERKLIRFVF  220 (233)
T ss_pred             CCCEEEEEEEEEEECCCCCCCCEEEEEEEEC--CCHHHHHHHHHHHH
T ss_conf             4000450038998537753363466678703--89889999999999


No 8  
>COG5581 c-di-GMP-binding protein [Signal transduction mechanisms]
Probab=95.37  E-value=0.24  Score=28.60  Aligned_cols=102  Identities=23%  Similarity=0.301  Sum_probs=71.8

Q ss_pred             HHHHHHHHCCCEEEEEEEEEEEEECC----CCCEEEEEEEECCCCEEEEECCCCCC---CCCEEEEEECCCC------CE
Q ss_conf             34322201062147999705799468----98302699987568549994278876---7974999995544------37
Q gi|254780885|r    6 HNLQFIDQRAFQRVKVDLKGRFLLFD----GTEYNCIVREISPGGLCIVCDVPMFL---VGERSIVFVEKVG------RI   72 (207)
Q Consensus         6 ~~~~~~drR~f~RV~v~l~GR~ll~d----~~E~~C~t~diSpgg~~l~~~~~~~~---~Gervv~Yld~iG------rl   72 (207)
                      -++.+..||.+-||.+.+..-|--.+    ...+--++.|+|.||+.+..+...+.   .|.+++-.+-..+      ..
T Consensus       103 e~lkriQRR~~fRvsa~l~~~y~~~~~~~d~~~lr~~~~DiS~GGm~~vl~~gl~~~l~e~~~~~~~~~~~~~d~~li~~  182 (233)
T COG5581         103 ETLKRIQRRRYFRVSAPLSPPYYVQNKLTDEEPLRFTLYDISAGGMGLVLEGGLSFRLHEGIRYVDALVDEGQDQQLISI  182 (233)
T ss_pred             HHHHHHHHHHHEEECCCCCCCEEECCCCCCCCCCEEEEEEECCCCHHEEECCCCCCCCCCCCEEEEEECCCCCCCCEEEE
T ss_conf             99889887664563420146455325667656512378860476320110777675767873787640105654000450


Q ss_pred             EEEEEEECC-------CCCEEEEEECCHHHHHHHHHHHHHHHC
Q ss_conf             699999308-------983899997698789999999998764
Q gi|254780885|r   73 EGKVVNFDS-------NRGYAVRIVTSENERRKLADKLIWLAN  108 (207)
Q Consensus        73 EG~V~r~~~-------~~GFav~l~~t~~kR~kLA~qLtWlan  108 (207)
                      +.+|++..-       .-||- =++++++-.++|..-..-+..
T Consensus       183 ~~~vv~~~k~e~~~~~r~~le-Fl~is~~~er~l~r~~F~lqr  224 (233)
T COG5581         183 SARVVRIRKDEKLGERRLGLE-FLEISPRIERKLIRFVFELQR  224 (233)
T ss_pred             EEEEEEECCCCCCCCEEEEEE-EECCCHHHHHHHHHHHHHHHH
T ss_conf             038998537753363466678-703898899999999999999


No 9  
>cd07705 Ig2_Necl-1 Second immunoglobulin (Ig)-like domain of nectin-like molcule-1 (Necl-1, also known as cell adhesion molecule3 (CADM3)). Ig2_Necl-1: second immunoglobulin (Ig)-like domain of nectin-like molcule-1 (Necl-1, also known as cell adhesion molecule3 (CADM3)). These nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 - Necl-5). These have an extracellular region containing three Ig-like domains, one transmembrane region, and one cytoplasmic region. The N-terminal Ig-like domain of the extracellular region belongs to the V-type subfamily of Ig domains, is essential to cell-cell adhesion, and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-1 and Necl-2 have Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-1 is specifically expressed in neural tissue and is important to the formation of synapses, axon bundles, and myel
Probab=85.16  E-value=0.29  Score=28.07  Aligned_cols=66  Identities=18%  Similarity=0.220  Sum_probs=42.4

Q ss_pred             HHHHHHHHHHCCCCCCCCHHCCCCCCCCCCCCCEEEEEE-----CCCCEEEEEEEEEECCCEEEECCCCCC
Q ss_conf             999999987642436750210256747777651368995-----799889899998742420455157789
Q gi|254780885|r   98 KLADKLIWLANKDDLHLQDCRAYGRKITRDREVDAQLVL-----NDNTKHSCKVIDISESGVSVSVDLQIE  163 (207)
Q Consensus        98 kLA~qLtWlanr~~l~l~e~R~h~R~vPr~~~~~~~l~l-----~DG~~~~criiDiS~SGAAi~~~~rp~  163 (207)
                      |=|++|+|+-+..++.-....--+--.++.-.+.|+|++     +||..++|+.-.-|+.|...++..++.
T Consensus        12 kPaA~I~W~kg~~el~~~~~~~~e~~~~~t~tvtS~l~~~~tr~Ddg~~~tC~a~h~al~~~~~~t~~~l~   82 (83)
T cd07705          12 KPAANIKWRKGDQELEGAPTSVLEDGNGKTFTVSSSVEFQVTREDDGAEITCSVGHESLHDSDRSTSQRIE   82 (83)
T ss_pred             CCCCEEEEECCCEECCCCCCCEECCCCCCEEEEEEEEEEEECCCCCCCEEEEEEECCCCCCCCCEEEEEEC
T ss_conf             68888899559989867774070068997699988999981210289789999848223797703589960


No 10 
>PRK11642 exoribonuclease R; Provisional
Probab=83.67  E-value=3.7  Score=21.31  Aligned_cols=74  Identities=11%  Similarity=0.059  Sum_probs=53.5

Q ss_pred             HHHHHHHCCCEEEEEEEEEEEEECCCCCEEEEEEEECCCCEEEEECCCCCC-------------CCCEEEEEE---CCCC
Q ss_conf             432220106214799970579946898302699987568549994278876-------------797499999---5544
Q gi|254780885|r    7 NLQFIDQRAFQRVKVDLKGRFLLFDGTEYNCIVREISPGGLCIVCDVPMFL-------------VGERSIVFV---EKVG   70 (207)
Q Consensus         7 ~~~~~drR~f~RV~v~l~GR~ll~d~~E~~C~t~diSpgg~~l~~~~~~~~-------------~Gervv~Yl---d~iG   70 (207)
                      .|+++++..  -+--+=.|+|.+|+..+.-.-+...++.|+.++.+...+.             -||+|.+.+   +.=|
T Consensus        58 ~L~~l~~~g--~l~~~r~~~y~~~~~~~lv~G~v~~~~~GfgFv~~e~~~eDifI~~~~l~~a~~GDrVlvr~~~~~r~g  135 (813)
T PRK11642         58 RLRAMERDG--QLVFTRRQCYALPERLDLLKGTVIGHRDGYGFLRVEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKG  135 (813)
T ss_pred             HHHHHHHCC--CEEECCCCCCCCCCCCCCEEEEEEECCCCCEEEECCCCCCCEEECHHHHCCCCCCCEEEEEEECCCCCC
T ss_conf             999999689--778748972367776785689999888877788707987770008467432679999999982477889


Q ss_pred             CEEEEEEEECCC
Q ss_conf             376999993089
Q gi|254780885|r   71 RIEGKVVNFDSN   82 (207)
Q Consensus        71 rlEG~V~r~~~~   82 (207)
                      |-||+|++++..
T Consensus       136 r~Eg~Vv~IleR  147 (813)
T PRK11642        136 RREARIVRVLVP  147 (813)
T ss_pred             CCCEEEEEEEEC
T ss_conf             861799999951


No 11 
>TIGR02266 gmx_TIGR02266 Myxococcus xanthus paralogous domain TIGR02266; InterPro: IPR011752   This domain is related to Type IV pilus assembly protein PilZ (IPR009875 from INTERPRO). It is found in at least 12 copies in Myxococcus xanthus DK 1622..
Probab=83.62  E-value=1.2  Score=24.19  Aligned_cols=62  Identities=16%  Similarity=0.306  Sum_probs=33.3

Q ss_pred             EEEE-CC-CCEEEEEEEEEECCCEEEECCCCCCCCCEEEE-----C-----CEEEEEEEEE---CC---EEEEEECCCCC
Q ss_conf             8995-79-98898999987424204551577899855897-----3-----4669999993---89---08999716778
Q gi|254780885|r  133 QLVL-ND-NTKHSCKVIDISESGVSVSVDLQIEMFSKVLF-----N-----DILGRVVRIF---PG---GIAIEFSSVQE  194 (207)
Q Consensus       133 ~l~l-~D-G~~~~criiDiS~SGAAi~~~~rp~iGs~V~v-----G-----~~~grVVRh~---~~---GfaVeF~~~q~  194 (207)
                      .+.+ ++ +.-...+.+|||.-|.-|.+...+++||.|++     |     ...|.|+.--   ++   |.||+|.+.+.
T Consensus         7 ~v~~q~~~~~f~~~~~~NlS~GGlF~~T~~~~~~GT~V~l~~~lpg~~~~~~~~g~V~w~~~~~~~~~~GmGvRF~~~d~   86 (97)
T TIGR02266         7 KVDFQETESEFLRDYSSNLSEGGLFIRTRKPLAVGTRVELKLTLPGGERPLELKGVVVWVREAADGAPPGMGVRFEDLDA   86 (97)
T ss_pred             EEEEECCCHHHHHHHHHCCCCCCEEEEECCCCCCCCEEEEEEEECCCCCEEEEEEEEEEECCCCCCCCCEEEEEECCCCH
T ss_conf             87643392356665431266782588707888789637999881899525788789998636888988447899610896


No 12 
>cd05885 Ig2_Necl-4 Second immunoglobulin (Ig)-like domain of nectin-like molecule-4  (Necl-4, also known as cell adhesion molecule 4 (CADM4)). Ig2_Necl-4: second immunoglobulin (Ig)-like domain of nectin-like molecule-4  (Necl-4, also known as cell adhesion molecule 4 (CADM4)). Nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1-Necl-5). These have an extracellular region containing three Ig-like domains, one transmembrane region, and one cytoplasmic region. Ig domains are likely to participate in ligand binding and recognition. Necl-4 is expressed on Schwann cells, and plays a key part in initiating peripheral nervous system (PNS) myelination.  In injured peripheral nerve cells, the mRNA signal for both Necl-4 and Necl-5 was observed to be elevated.  Necl-4 participates in cell-cell adhesion and is proposed to play a role in tumor suppression.
Probab=74.74  E-value=0.64  Score=25.96  Aligned_cols=64  Identities=14%  Similarity=0.206  Sum_probs=40.6

Q ss_pred             HHHHHHHHHHHCCCCCCCCHHCCCCCCCCCCCCCEEEEE-----ECCCCEEEEEEEEEECCCEEEECCCCCC
Q ss_conf             999999998764243675021025674777765136899-----5799889899998742420455157789
Q gi|254780885|r   97 RKLADKLIWLANKDDLHLQDCRAYGRKITRDREVDAQLV-----LNDNTKHSCKVIDISESGVSVSVDLQIE  163 (207)
Q Consensus        97 ~kLA~qLtWlanr~~l~l~e~R~h~R~vPr~~~~~~~l~-----l~DG~~~~criiDiS~SGAAi~~~~rp~  163 (207)
                      -|-|++|+|+-|.+++.-  ..... -.++.-.+.++|.     -+||..+.|+.-+-++.|-++....++.
T Consensus        11 SkPaA~i~W~r~~kel~~--~~~~~-~ngk~~tvsS~l~f~~~r~DdG~~~tC~a~h~al~~~~~~~~~~Ld   79 (80)
T cd05885          11 SKPAATLRWYRDRKELKG--VISQQ-ENGKTVSVSNTIRFPVDRKDDGAILSCEASHPALVSQKKQTQYSLD   79 (80)
T ss_pred             CCCCCEEEEEECCEECCC--EEEEC-CCCCEEEEEEEEEEECCCHHCCCEEEEEEECCCCCCCCEEEEEEEC
T ss_conf             968768799889999767--02671-6998899988899857332289599999748565898616679972


No 13 
>cd05884 Ig2_Necl-3 Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2)). Ig2_Necl-3: second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2)). Nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 - Necl-5). These have an extracellular region containing three Ig-like domains, one transmembrane region, and one cytoplasmic region. Necl-3 has been shown to accumulate in tissues of the central and peripheral nervous system, where it is expressed in ependymal cells and myelinated axons.  It is observed at the interface between the axon shaft and the myelin sheath. Ig domains are likely to participate in ligand binding and recognition.
Probab=71.58  E-value=1.2  Score=24.39  Aligned_cols=59  Identities=17%  Similarity=0.218  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHCCCCCCCCHHCCCCCCCCCCCCCEEEEEE-----CCCCEEEEEEEEEECCCEE
Q ss_conf             9999999987642436750210256747777651368995-----7998898999987424204
Q gi|254780885|r   97 RKLADKLIWLANKDDLHLQDCRAYGRKITRDREVDAQLVL-----NDNTKHSCKVIDISESGVS  155 (207)
Q Consensus        97 ~kLA~qLtWlanr~~l~l~e~R~h~R~vPr~~~~~~~l~l-----~DG~~~~criiDiS~SGAA  155 (207)
                      .|=|++|+|+-|..++.-.-....+--.++.-.+.|+|.|     +||..+.|++-.-++.|..
T Consensus        11 SKPaA~I~W~rg~~el~~~~~~~e~~~~gK~ftvtS~L~~~~~~~Ddg~~~tC~a~H~AL~~~~   74 (83)
T cd05884          11 SKPAADIRWFKNDKEIKDVKYLKEEDANRKTFTVSSTLDFRVDRSDDGVAIICRVDHESLNATP   74 (83)
T ss_pred             CCCCCEEEEEECCEECCCCCEEEEECCCCCEEEEEEEEEEECCCCCCCCEEEEEEECCCCCCCH
T ss_conf             9676387998699998784036674478878999889998621335996899997280226880


No 14 
>COG0179 MhpD 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=52.32  E-value=19  Score=16.94  Aligned_cols=14  Identities=14%  Similarity=0.363  Sum_probs=7.9

Q ss_pred             CEEEEEECCHHHHH
Q ss_conf             38999976987899
Q gi|254780885|r   84 GYAVRIVTSENERR   97 (207)
Q Consensus        84 GFav~l~~t~~kR~   97 (207)
                      ||.+-...|.|---
T Consensus       140 GYti~nD~T~Rd~Q  153 (266)
T COG0179         140 GYTIGNDVTARDLQ  153 (266)
T ss_pred             EEEEEEECCHHCCH
T ss_conf             77666651200123


No 15 
>cd05761 Ig2_Necl-1-4_like Second immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 - Necl-4 (also known as cell adhesion molecules CADM3, CADM1, CADM2, and CADM4, respectively). Ig2_Necl-1-4_like: domain similar to the second immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 (also known as cell adhesion molecule 3 (CADM3)), Necl-2 (CADM1), Necl-3 (CADM2) and Necl-4 (CADM4). These nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 - Necl-5). These have an extracellular region containing three Ig-like domains, one transmembrane region, and one cytoplasmic region. The N-terminal Ig-like domain of the extracellular region belongs to the V-type subfamily of Ig domains, is essential to cell-cell adhesion, and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-1 and Necl-2 have Ca(2+)-independent homophilic and heterophilic cell-cel
Probab=52.03  E-value=3.2  Score=21.71  Aligned_cols=61  Identities=15%  Similarity=0.229  Sum_probs=38.7

Q ss_pred             HHHHHHHHHHCCCCCCCCHHCCCCCCCCCCC---CCEEEEE-----ECCCCEEEEEEEEEECCCEEEECCCCC
Q ss_conf             9999999876424367502102567477776---5136899-----579988989999874242045515778
Q gi|254780885|r   98 KLADKLIWLANKDDLHLQDCRAYGRKITRDR---EVDAQLV-----LNDNTKHSCKVIDISESGVSVSVDLQI  162 (207)
Q Consensus        98 kLA~qLtWlanr~~l~l~e~R~h~R~vPr~~---~~~~~l~-----l~DG~~~~criiDiS~SGAAi~~~~rp  162 (207)
                      |=|++|+|+-+.+.+.  ..  +....+.+.   .+.++|+     -+||..+.|+.-+-++-|.+++...++
T Consensus        12 ~P~A~ItW~~~~~~l~--~~--~~~~~~~~~~~~tvtS~L~~~p~~~D~G~~ltC~a~n~al~~~~~e~~~~L   80 (82)
T cd05761          12 KPAATIRWFKGDKELK--GV--KLKEEDENGKTFTVTSSLRFQVDREDDGAPIICRVDHPALKSTDKQTQQVL   80 (82)
T ss_pred             CCCCEEEEEECCEECC--CC--EEEEECCCCCEEEEEEEEEEECCHHHCCCEEEEEEECCCCCCCCCEEEEEE
T ss_conf             2887889986998985--72--046765899889999999997775669989999984867899971789998


No 16 
>TIGR02305 HpaG-N-term 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, N-terminal subunit; InterPro: IPR012686    This entry represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation . In Escherichia coli and some other species this enzyme is encoded by a single polypeptide containing both this domain and the closely related C-terminal domain (IPR012684 from INTERPRO). In other species such as Pasteurella multocida these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).; GO: 0008704 5-carboxymethyl-2-hydroxymuconate delta-isomerase activity, 0018800 5-oxopent-3-ene-125-tricarboxylate decarboxylase activity.
Probab=49.38  E-value=16  Score=17.47  Aligned_cols=35  Identities=23%  Similarity=0.373  Sum_probs=23.0

Q ss_pred             ECCCCEEEEECCC---CCCCCCEEEEEECCCCCEEEEE
Q ss_conf             7568549994278---8767974999995544376999
Q gi|254780885|r   42 ISPGGLCIVCDVP---MFLVGERSIVFVEKVGRIEGKV   76 (207)
Q Consensus        42 iSpgg~~l~~~~~---~~~~Gervv~Yld~iGrlEG~V   76 (207)
                      +++|++.++.--.   .-..|+||.+-+|.+|.|+++|
T Consensus       169 L~~GDvll~Gt~~~~~~v~~Gd~V~v~~~~~g~L~N~v  206 (206)
T TIGR02305       169 LEAGDVLLLGTPEERVKVGPGDRVRVEIEGLGELENEV  206 (206)
T ss_pred             CCCCCEEEECCCCCCEECCCCCEEEEEECCCCCCCCCC
T ss_conf             27698899706788624278878886101676367789


No 17 
>pfam08205 C2-set_2 CD80-like C2-set immunoglobulin domain. These domains belong to the immunoglobulin superfamily.
Probab=45.27  E-value=7.1  Score=19.56  Aligned_cols=56  Identities=18%  Similarity=0.230  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHCCCCCCCCHHCCCCCCCCCCCCCEEEEEE-----CCCCEEEEEEEEEECCC
Q ss_conf             999999987642436750210256747777651368995-----79988989999874242
Q gi|254780885|r   98 KLADKLIWLANKDDLHLQDCRAYGRKITRDREVDAQLVL-----NDNTKHSCKVIDISESG  153 (207)
Q Consensus        98 kLA~qLtWlanr~~l~l~e~R~h~R~vPr~~~~~~~l~l-----~DG~~~~criiDiS~SG  153 (207)
                      |=|.+|+|+-+-..+.-........-.+..-.+.++|++     ++|..+.|++-.-+++|
T Consensus        27 ~P~a~i~W~~~~~~l~~~~~~~~~~~~~~~~t~~S~L~~~pt~~D~g~~l~C~a~~~al~~   87 (89)
T pfam08205        27 KPAPRITWYLDGRELEAITTSSEQDPESGLYTVTSTLKLVPSREDHGRSLTCQVSYGALRG   87 (89)
T ss_pred             CCCCEEEEEECCCCCCCCEEEEEECCCCCCEEEEEEEEEECCHHHCCCEEEEEEECCCCCC
T ss_conf             7898689996995123623268775889769999999997567998989899994567788


No 18 
>TIGR00037 eIF_5A translation initiation factor eIF-5A; InterPro: IPR001884   Translation initiation factor 5A (IF-5A) is reported to be involved in the first step of peptide bond formation in translation, to be involved in cell-cycle regulation and to be a cofactor for the Rev and Rex transactivator proteins of human immunodeficiency virus-1 and T-cell leukaemia virus I, respectively , , . IF-5A contains an unusual amino acid, hypusine N-epsilon-(4-aminobutyl-2-hydroxy)lysine), that is required for its function. The first step in the post-translational modification of lysine to hypusine is catalyzed by the enzyme deoxyhypusine synthase, the structure of which has been reported.    The crystal structure of IF-5A from the archaeon Pyrobaculum aerophilum has been determined to 1.75 A. Unmodified P. aerophilum IF-5A is found to be a beta structure with two domains and three separate hydrophobic cores. The lysine (Lys42) that is post-translationally modified by deoxyhypusine synthase is found at one end of the IF-5A molecule in a turn between beta strands beta4 and beta5; this lysine residue is freely solvent accessible. The C-terminal domain is found to be homologous to the cold-shock protein CspA of E. coli, which has a well characterised RNA-binding fold, suggesting that IF-5A is involved in RNA binding . ; GO: 0003743 translation initiation factor activity, 0006413 translational initiation.
Probab=44.97  E-value=8  Score=19.24  Aligned_cols=10  Identities=30%  Similarity=0.531  Sum_probs=7.3

Q ss_pred             EEEEEEEECC
Q ss_conf             0269998756
Q gi|254780885|r   35 YNCIVREISP   44 (207)
Q Consensus        35 ~~C~t~diSp   44 (207)
                      -||..+|||.
T Consensus        23 ~PC~IvdiS~   32 (137)
T TIGR00037        23 EPCKIVDIST   32 (137)
T ss_pred             CCCEEEECCC
T ss_conf             6760676131


No 19 
>TIGR02303 HpaG-C-term 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit; InterPro: IPR012684    This entry represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation . In Escherichia coli and some other species, this enzyme is encoded by a single polypeptide containing both this domain and the closely related N-terminal domain (IPR012686 from INTERPRO). In other species such as Pasteurella multocida, these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).; GO: 0008704 5-carboxymethyl-2-hydroxymuconate delta-isomerase activity, 0018800 5-oxopent-3-ene-125-tricarboxylate decarboxylase activity.
Probab=43.94  E-value=26  Score=16.14  Aligned_cols=42  Identities=24%  Similarity=0.392  Sum_probs=31.1

Q ss_pred             EEEEEEEECCCCEEEEECCCCC----CCCCEEEEEECCCCCEEEEEE
Q ss_conf             0269998756854999427887----679749999955443769999
Q gi|254780885|r   35 YNCIVREISPGGLCIVCDVPMF----LVGERSIVFVEKVGRIEGKVV   77 (207)
Q Consensus        35 ~~C~t~diSpgg~~l~~~~~~~----~~Gervv~Yld~iGrlEG~V~   77 (207)
                      |=-...-+.||++-++. .|-|    ++||-|.+=++++|+||-.|+
T Consensus       202 ylS~~mTL~PgD~ilTG-TPKG~~dv~pGD~v~~eiEGvG~L~N~i~  247 (249)
T TIGR02303       202 YLSEFMTLEPGDVILTG-TPKGLSDVKPGDVVRLEIEGVGKLENPIV  247 (249)
T ss_pred             HHHHCCCCCCCCEEEEC-CCCCCCCCCCCCEEEEEECCCCCEECCCC
T ss_conf             86310247856488705-88875223558789997700262103110


No 20 
>COG0809 QueA S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (queuine synthetase) [Translation, ribosomal structure and biogenesis]
Probab=43.40  E-value=26  Score=16.09  Aligned_cols=35  Identities=14%  Similarity=0.207  Sum_probs=25.9

Q ss_pred             ECCCCCCCCCEEEECC-EEEEEEEEECC-EEEEEECC
Q ss_conf             5157789985589734-66999999389-08999716
Q gi|254780885|r  157 SVDLQIEMFSKVLFND-ILGRVVRIFPG-GIAIEFSS  191 (207)
Q Consensus       157 ~~~~rp~iGs~V~vG~-~~grVVRh~~~-GfaVeF~~  191 (207)
                      ....++-.|+.+.+|. +.+.|+-..++ ++-++|..
T Consensus        97 ~~~kr~k~G~~i~f~~~l~a~v~e~~~~g~~~l~F~~  133 (348)
T COG0809          97 KPSKRLKAGDEIYFGDGLKATVLERLEHGLRLLEFDY  133 (348)
T ss_pred             CCCCCCCCCCEEEECCCCEEEEEEECCCCEEEEEEEC
T ss_conf             3256788899899479826999996288529999945


No 21 
>KOG1989 consensus
Probab=40.96  E-value=29  Score=15.85  Aligned_cols=28  Identities=18%  Similarity=0.209  Sum_probs=12.3

Q ss_pred             CCCEEEEEEEECCCCCEEEEEECCHHHH
Q ss_conf             4437699999308983899997698789
Q gi|254780885|r   69 VGRIEGKVVNFDSNRGYAVRIVTSENER   96 (207)
Q Consensus        69 iGrlEG~V~r~~~~~GFav~l~~t~~kR   96 (207)
                      +|+.--+|-++++..||+.-.-+...+-
T Consensus        34 Vg~~~v~V~~vLAEGGFa~VYla~~~~~   61 (738)
T KOG1989          34 VGSHRVTVEKVLAEGGFAQVYLAQDVKG   61 (738)
T ss_pred             ECCEEEEEEEEECCCCCEEEEEEEECCC
T ss_conf             7877899999971477279999885388


No 22 
>KOG3591 consensus
Probab=40.82  E-value=29  Score=15.84  Aligned_cols=79  Identities=11%  Similarity=0.109  Sum_probs=44.0

Q ss_pred             CCCCCEEEEEECCHHHHHHHHHHHH----HHHCCCCCCCCHHCCCCCCCCCCCCCEEEEEECCCCEEEEEEEEEECCCEE
Q ss_conf             0898389999769878999999999----876424367502102567477776513689957998898999987424204
Q gi|254780885|r   80 DSNRGYAVRIVTSENERRKLADKLI----WLANKDDLHLQDCRAYGRKITRDREVDAQLVLNDNTKHSCKVIDISESGVS  155 (207)
Q Consensus        80 ~~~~GFav~l~~t~~kR~kLA~qLt----Wlanr~~l~l~e~R~h~R~vPr~~~~~~~l~l~DG~~~~criiDiS~SGAA  155 (207)
                      ..+++|.|.|.+..=|-+.|-=++.    -...+|+    |.+-.--++-|.  -.-..+|+.|.-..-=--.||-.|.-
T Consensus        69 ~~~~~F~V~lDV~~F~PeEl~Vk~~~~~l~V~gkHe----er~d~~G~v~R~--F~R~y~LP~~vdp~~V~S~LS~dGvL  142 (173)
T KOG3591          69 NDKDKFEVNLDVHQFKPEELKVKTDDNTLEVEGKHE----EKEDEHGYVSRS--FVRKYLLPEDVDPTSVTSTLSSDGVL  142 (173)
T ss_pred             CCCCCEEEEEECCCCCCCCCEEEECCCEEEEEEEEC----CCCCCCCEEEEE--EEEEECCCCCCCHHHEEEEECCCCEE
T ss_conf             189867999880247655118995798899986606----461799769889--88876699998950627863799408


Q ss_pred             EECCCCCCC
Q ss_conf             551577899
Q gi|254780885|r  156 VSVDLQIEM  164 (207)
Q Consensus       156 i~~~~rp~i  164 (207)
                      .-....|+.
T Consensus       143 tI~ap~~~~  151 (173)
T KOG3591         143 TIEAPKPPP  151 (173)
T ss_pred             EEECCCCCC
T ss_conf             997358887


No 23 
>PRK13613 lipoprotein LpqB; Provisional
Probab=40.30  E-value=8.6  Score=19.03  Aligned_cols=20  Identities=10%  Similarity=0.140  Sum_probs=17.4

Q ss_pred             ECCHHHHHHHHHHHHHHHCC
Q ss_conf             76987899999999987642
Q gi|254780885|r   90 VTSENERRKLADKLIWLANK  109 (207)
Q Consensus        90 ~~t~~kR~kLA~qLtWlanr  109 (207)
                      .++++.|.+||+||.|=.+.
T Consensus       268 ~~~~~~r~~maAQL~~TL~~  287 (603)
T PRK13613        268 RAGPRRCFGMAAQLLFTLKD  287 (603)
T ss_pred             CCCHHHHHHHHHHHHHHHHC
T ss_conf             37999999999999998531


No 24 
>cd05759 Ig2_KIRREL3-like Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2). Ig2_KIRREL3-like: domain similar to the second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2). This protein has five Ig-like domains, one transmembrane domain, and a cytoplasmic tail. Included in this group is mammalian Kirrel (Neph1), Kirrel2 (Neph3), and Drosophila RST (irregular chiasm C-roughest) protein. These proteins contain multiple Ig domains, have properties of cell adhesion molecules, and are important in organ development.
Probab=39.69  E-value=6.3  Score=19.89  Aligned_cols=53  Identities=13%  Similarity=0.303  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHCCCCCCCCHHCCCCCCCCCCC--CCEEEEEE-----CCCCEEEEEEEEEECC
Q ss_conf             9999999876424367502102567477776--51368995-----7998898999987424
Q gi|254780885|r   98 KLADKLIWLANKDDLHLQDCRAYGRKITRDR--EVDAQLVL-----NDNTKHSCKVIDISES  152 (207)
Q Consensus        98 kLA~qLtWlanr~~l~l~e~R~h~R~vPr~~--~~~~~l~l-----~DG~~~~criiDiS~S  152 (207)
                      |=|++|+|+-+...+.  ..-...-..+.++  .+.++|++     +||..+.|+.-+-.+.
T Consensus        12 kPaA~ItW~r~g~~l~--~~~~~~~~~~dgk~~tt~S~L~~~P~~~DdG~~~tC~A~n~alp   71 (82)
T cd05759          12 KPAAEIIWFRDGEVLD--GATYSKELLKDGKRETTVSTLPITPSDHDTGRTFTCRARNEALP   71 (82)
T ss_pred             CCCCEEEEEECCEEEE--CCEEEEEECCCCCEEEEEEEEEEECCCHHCCCEEEEEEECCCCC
T ss_conf             1798999999999920--63367777379988779999999644144898999998485589


No 25 
>cd05883 Ig2_Necl-2 Second immunoglobulin (Ig)-like domain of nectin-like molecule 2 (also known as cell adhesion molecule 1 (CADM1)). Ig2_Necl-2: second immunoglobulin (Ig)-like domain of nectin-like molecule 2 (also known as cell adhesion molecule 1 (CADM1)). Nectin-like molecules (Necls) have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 - Necl-5). These have an extracellular region containing three Ig-like domains, one transmembrane region, and one cytoplasmic region. Necl-2 has Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-1 is expressed in a wide variety of tissues, and is a putative tumour suppressor gene, which is downregulated in aggressive neuroblastoma. Ig domains are likely to participate in ligand binding and recognition.
Probab=37.89  E-value=8.3  Score=19.16  Aligned_cols=54  Identities=22%  Similarity=0.263  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHHCCCCCCCCHHCCCCCCCCCCCCCEEEEEE-----CCCCEEEEEEEEEECC
Q ss_conf             9999999987642436750210256747777651368995-----7998898999987424
Q gi|254780885|r   97 RKLADKLIWLANKDDLHLQDCRAYGRKITRDREVDAQLVL-----NDNTKHSCKVIDISES  152 (207)
Q Consensus        97 ~kLA~qLtWlanr~~l~l~e~R~h~R~vPr~~~~~~~l~l-----~DG~~~~criiDiS~S  152 (207)
                      .|=|++|.|+-++.++.-....-..  ..+.=.+.|+|++     +||..++|++-.-|+.
T Consensus        11 SKPaA~I~W~kg~~El~g~~~~~e~--~~k~fTv~Ssl~~~v~r~DDg~~~tC~a~Hpal~   69 (82)
T cd05883          11 SKPAATIRWFKGNKELTGKSTVEET--WSRMFTVTSQLMLKVTKEDDGVPVICLVDHPAVK   69 (82)
T ss_pred             CCCCCEEEEEECCEECCCCCCHHHC--CCCEEEEEEEEEEEECCCCCCCEEEEEECCCCCC
T ss_conf             9676588997299886672511214--5865999789998714235993889994287458


No 26 
>cd06475 ACD_HspB1_like Alpha crystallin domain (ACD) found in mammalian small (s)heat shock protein (Hsp)-27 (also denoted HspB1 in human) and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Hsp27 shows enhanced synthesis in response to stress. It is a molecular chaperone which interacts with a large number of different proteins. It is found in many types of human cells including breast, uterus, cervix, platelets and cancer cells. Hsp27 has diverse cellular functions including, chaperoning, regulation of actin polymerization, keratinocyte differentiation, regulation of inflammatory pathways in keratinocytes, and protection from oxidative stress through modulating glutathione levels. It is also a subunit of AUF1-containing protein complexes. It has been linked to several transduction pathways regulating cellular functions including differentiat
Probab=37.57  E-value=31  Score=15.67  Aligned_cols=30  Identities=20%  Similarity=0.386  Sum_probs=15.4

Q ss_pred             EEEEEEEECCCCCEEEEEEEECCCCEEEEE
Q ss_conf             970579946898302699987568549994
Q gi|254780885|r   22 DLKGRFLLFDGTEYNCIVREISPGGLCIVC   51 (207)
Q Consensus        22 ~l~GR~ll~d~~E~~C~t~diSpgg~~l~~   51 (207)
                      +..=+|.||+.-+-...+..+|..|+..+.
T Consensus        54 ~F~R~~~LP~~vd~~~v~s~Ls~dG~L~I~   83 (86)
T cd06475          54 CFTRKYTLPPGVDPTAVTSSLSPDGILTVE   83 (86)
T ss_pred             EEEEEECCCCCCCHHHEEEEECCCCEEEEE
T ss_conf             999953398998977869974899889998


No 27 
>cd06479 ACD_HspB7_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB7, also known as cardiovascular small heat shock protein (cvHsp), and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. HspB7 is a 25-kDa protein, preferentially expressed in heart and skeletal muscle. It binds the cytoskeleton protein alpha-filamin (also known as actin-binding protein 280). The expression of HspB7 is increased during rat muscle aging.  Its expression is also modulated in obesity implicating this protein in this and related metabolic disorders. As the human gene encoding HspB7 is mapped to chromosome 1p36.23-p34.3 it is a positional candidate for several dystrophies and myopathies.
Probab=33.11  E-value=38  Score=15.09  Aligned_cols=29  Identities=7%  Similarity=0.147  Sum_probs=14.6

Q ss_pred             EEEEEEECCCCCEEEEEEEECCCCEEEEE
Q ss_conf             70579946898302699987568549994
Q gi|254780885|r   23 LKGRFLLFDGTEYNCIVREISPGGLCIVC   51 (207)
Q Consensus        23 l~GR~ll~d~~E~~C~t~diSpgg~~l~~   51 (207)
                      ..=+|.||++-|-.-.+..+|+.|+..+.
T Consensus        50 F~Rry~LP~~vdp~~v~SsLs~DGvLtI~   78 (81)
T cd06479          50 FTHKCQLPEDVDPTSVSSSLGEDGTLTIK   78 (81)
T ss_pred             EEEEECCCCCCCCCCEEEEECCCCEEEEE
T ss_conf             99965299993940659984799489998


No 28 
>cd06476 ACD_HspB2_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB2/heat shock 27kDa protein 2 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits.  HspB2 is preferentially and constitutively expressed in skeletal muscle and heart. HspB2 shows homooligomeric activity and forms aggregates in muscle cytosol. Although its expression is not induced by heat shock, it redistributes to the insoluble fraction in response to heat shock. In the mouse heart, HspB2 plays a role in maintaining energetic balance, by protecting cardiac energetics during ischemia/reperfusion, and allowing  for increased work during acute inotropic challenge. hHspB2 [previously also known as myotonic dystrophy protein kinase (DMPK) binding protein (MKBP)]  is selectively up-regulated in skeletal muscles from myotonic dystrophy patients.
Probab=32.61  E-value=38  Score=15.07  Aligned_cols=33  Identities=12%  Similarity=0.180  Sum_probs=22.0

Q ss_pred             EEEEEEEEEEECCCCCEEEEEEEECCCCEEEEE
Q ss_conf             799970579946898302699987568549994
Q gi|254780885|r   19 VKVDLKGRFLLFDGTEYNCIVREISPGGLCIVC   51 (207)
Q Consensus        19 V~v~l~GR~ll~d~~E~~C~t~diSpgg~~l~~   51 (207)
                      +.=+..=+|.||++.+-.-.+..+|..|+..+.
T Consensus        48 v~R~F~R~y~LP~~vd~~~v~S~Ls~DGvL~I~   80 (83)
T cd06476          48 VSREFTRTYILPMDVDPLLVRASLSHDGILCIQ   80 (83)
T ss_pred             EEEEEEEEEECCCCCCHHHEEEECCCCCEEEEE
T ss_conf             999999976388995977909963899749998


No 29 
>TIGR02037 degP_htrA_DO protease Do; InterPro: IPR011782   Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .   Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This family consists serine peptidases belonging to MEROPS peptidase family S1, subfamily S1C (protease Do, clan PA(S)). They are variously designated DegP, DegQ, heat shock protein HtrA, MucD and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in Escherichia coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens . The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures .; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis.
Probab=32.50  E-value=39  Score=15.03  Aligned_cols=15  Identities=20%  Similarity=0.476  Sum_probs=13.1

Q ss_pred             EEEECCCCEEEEEEE
Q ss_conf             899579988989999
Q gi|254780885|r  133 QLVLNDNTKHSCKVI  147 (207)
Q Consensus       133 ~l~l~DG~~~~crii  147 (207)
                      +++|.||++|.++||
T Consensus       118 ~V~L~DgrefkAklv  132 (484)
T TIGR02037       118 TVTLSDGREFKAKLV  132 (484)
T ss_pred             EEEECCCCEEEEEEE
T ss_conf             999459948556886


No 30 
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=30.98  E-value=34  Score=15.43  Aligned_cols=18  Identities=22%  Similarity=0.368  Sum_probs=14.4

Q ss_pred             EECCCCEEEEEEEEEECC
Q ss_conf             957998898999987424
Q gi|254780885|r  135 VLNDNTKHSCKVIDISES  152 (207)
Q Consensus       135 ~l~DG~~~~criiDiS~S  152 (207)
                      .+.-|+.|.||||+.|.-
T Consensus        46 ~fk~Gs~H~~RVig~s~~   63 (71)
T cd05696          46 PFKAGTTHKARIIGYSPM   63 (71)
T ss_pred             CCCCCCEEEEEEEECCCC
T ss_conf             864799888999834743


No 31 
>PRK10929 hypothetical protein; Provisional
Probab=30.12  E-value=25  Score=16.25  Aligned_cols=29  Identities=28%  Similarity=0.446  Sum_probs=14.4

Q ss_pred             CCEEEECCCCCCCCCEEEECCEEEEEEEE
Q ss_conf             42045515778998558973466999999
Q gi|254780885|r  152 SGVSVSVDLQIEMFSKVLFNDILGRVVRI  180 (207)
Q Consensus       152 SGAAi~~~~rp~iGs~V~vG~~~grVVRh  180 (207)
                      ||--+--|....||..||+|+..|.|-|.
T Consensus       926 SGlIiLFErPiRiGD~VTi~~~sGtVskI  954 (1109)
T PRK10929        926 SGLIILFEKPIRIGDTVTIRDLTGSVTKI  954 (1109)
T ss_pred             HHHHHHHCCCCCCCCEEEECCCCCEEEEE
T ss_conf             66898831671247668987845447778


No 32 
>PRK11281 potassium efflux protein KefA; Provisional
Probab=29.10  E-value=26  Score=16.11  Aligned_cols=29  Identities=21%  Similarity=0.340  Sum_probs=14.2

Q ss_pred             CCEEEECCCCCCCCCEEEECCEEEEEEEE
Q ss_conf             42045515778998558973466999999
Q gi|254780885|r  152 SGVSVSVDLQIEMFSKVLFNDILGRVVRI  180 (207)
Q Consensus       152 SGAAi~~~~rp~iGs~V~vG~~~grVVRh  180 (207)
                      ||--+--|....||..||+|+..|.|-|.
T Consensus       928 SGlIiLFErPiRiGD~vTi~~~sGtVskI  956 (1107)
T PRK11281        928 SGLIILFERPVRIGDTVTIGTFSGTVSKI  956 (1107)
T ss_pred             HHHHHHHCCCCCCCCEEEECCCCCEEEEE
T ss_conf             67898841671247668987845447778


No 33 
>cd05853 Ig6_Contactin-4 Sixth Ig domain of contactin-4. Ig6_Contactin-4: sixth Ig domain of the neural cell adhesion molecule contactin-4. Contactins are neural cell adhesion molecules, and are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. The different contactins show different expression patterns in the central nervous system. Highest expresson of contactin-4 is in testes, thyroid, small intestine, uterus and brain. Contactin-4 plays a role in the response of neuroblastoma cells to differentiating agents, such as retinoids. The contactin 4 gene is associated with cerebellar degeneration in spinocerebellar ataxia type 16.
Probab=29.03  E-value=20  Score=16.77  Aligned_cols=45  Identities=18%  Similarity=0.159  Sum_probs=31.2

Q ss_pred             HHHHHCCCCCCCCHHCCC-CCCCCC---CCCCEEEEEECCCCEEEEEEE
Q ss_conf             998764243675021025-674777---765136899579988989999
Q gi|254780885|r  103 LIWLANKDDLHLQDCRAY-GRKITR---DREVDAQLVLNDNTKHSCKVI  147 (207)
Q Consensus       103 LtWlanr~~l~l~e~R~h-~R~vPr---~~~~~~~l~l~DG~~~~crii  147 (207)
                      .+|..|-+...+..+=.| +|+-..   +.-....++|.++.+|.|-+-
T Consensus        19 f~W~~nG~~Idf~~~~~hyer~~~~~s~gdL~I~n~ql~haG~Y~C~aq   67 (85)
T cd05853          19 FTWSFNGHLIDFQKDGDHFERVGGQDSAGDLMIRSIQLKHAGKYVCMVQ   67 (85)
T ss_pred             EEEEECCEEEECCCCCCCEEEEECCCCCCCEEEEECCHHCCCEEEEEEE
T ss_conf             9998999996655788513897145786738999554101948899987


No 34 
>pfam10128 OpcA_G6PD_assem Glucose-6-phosphate dehydrogenase subunit. Members of this family are found in various prokaryotic OpcA and glucose-6-phosphate dehydrogenase proteins. The exact function of the domain is, as yet, unknown.
Probab=28.91  E-value=34  Score=15.43  Aligned_cols=12  Identities=25%  Similarity=0.224  Sum_probs=6.5

Q ss_pred             CCEEEEEEEECC
Q ss_conf             830269998756
Q gi|254780885|r   33 TEYNCIVREISP   44 (207)
Q Consensus        33 ~E~~C~t~diSp   44 (207)
                      .||||+++-+.+
T Consensus         7 ~ehPcRvIvl~~   18 (267)
T pfam10128         7 REHPCRVIVLVL   18 (267)
T ss_pred             HHCCCEEEEEEC
T ss_conf             649975999937


No 35 
>cd05854 Ig6_Contactin-2 Sixth Ig domain of contactin-2. Ig6_Contactin-2: Sixth Ig domain of the neural cell adhesion molecule contactin-2-like. Contactins are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. Contactin-2 (TAG-1, axonin-1) facilitates cell adhesion by homophilic binding between molecules in apposed membranes. It may play a part in the neuronal processes of neurite outgrowth, axon guidance and fasciculation, and neuronal migration. The first four Ig domains form the intermolecular binding fragment, which arranges as a compact U-shaped module by contacts between IG domains 1 and 4, and domains 2 and 3. The different contactins show different expression patterns in the central nervous system. During development and in adulthood, contactin-2 is transiently expressed in subsets of central and peripheral neurons. Contactin-2 is also expressed in retinal amacrine cells in the developing c
Probab=28.30  E-value=16  Score=17.39  Aligned_cols=46  Identities=13%  Similarity=0.190  Sum_probs=29.8

Q ss_pred             HHHHHCCCCCCCCHHCCCCCCCCCC----CCCEEEEEECCCCEEEEEEEE
Q ss_conf             9987642436750210256747777----651368995799889899998
Q gi|254780885|r  103 LIWLANKDDLHLQDCRAYGRKITRD----REVDAQLVLNDNTKHSCKVID  148 (207)
Q Consensus       103 LtWlanr~~l~l~e~R~h~R~vPr~----~~~~~~l~l~DG~~~~criiD  148 (207)
                      .+|+.|-+...+....+|-+.+...    --....+.+.|+.+|+|-.-.
T Consensus        19 ~tW~~dg~~Idf~~~~~h~~~~~~~~~~g~L~I~n~ql~d~G~YtC~A~T   68 (85)
T cd05854          19 FTWSLDDFPIDLDKPNGHYRRMEVKETIGDLVIVNAQLSHAGTYTCTAQT   68 (85)
T ss_pred             EEEEECCEEEECCCCCCCEEEECCCCCCCCEEEECCCCCCCCEEEEEEEC
T ss_conf             99988998920456877479802676534089955650259599999872


No 36 
>cd06480 ACD_HspB8_like Alpha-crystallin domain (ACD) found in mammalian 21.6 KDa small heat shock protein (sHsp) HspB8, also denoted as Hsp22 in humans, and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. A chaperone complex formed of HspB8 and Bag3 stimulates degradation of protein complexes by macroautophagy. HspB8 also forms complexes with Hsp27 (HspB1), MKBP (HspB2), HspB3, alphaB-crystallin (HspB5), Hsp20 (HspB6), and cvHsp (HspB7). These latter interactions may depend on phosphorylation of the respective partner sHsp. HspB8 may participate in the regulation of cell proliferation, cardiac hypertrophy, apoptosis, and carcinogenesis. Point mutations in HspB8 have been correlated with the development of several congenital neurological diseases, including Charcot Marie tooth disease and distal motor neuropathy type II.
Probab=27.31  E-value=48  Score=14.48  Aligned_cols=33  Identities=21%  Similarity=0.310  Sum_probs=23.8

Q ss_pred             EEEEEEEEEEECCCCCEEEEEEEECCCCEEEEE
Q ss_conf             799970579946898302699987568549994
Q gi|254780885|r   19 VKVDLKGRFLLFDGTEYNCIVREISPGGLCIVC   51 (207)
Q Consensus        19 V~v~l~GR~ll~d~~E~~C~t~diSpgg~~l~~   51 (207)
                      |.=+..=+|+||+.-+-...+..+|..|+..+.
T Consensus        56 vsR~F~Rky~LP~~vd~~~v~S~LS~dGvLtI~   88 (91)
T cd06480          56 VSKNFTKKIQLPPEVDPVTVFASLSPEGLLIIE   88 (91)
T ss_pred             EEEEEEEEECCCCCCCHHHEEEECCCCCEEEEE
T ss_conf             999999967089997975829963899639997


No 37 
>PTZ00328 eukaryotic initiation factor 5a; Provisional
Probab=26.53  E-value=35  Score=15.34  Aligned_cols=73  Identities=18%  Similarity=0.107  Sum_probs=39.9

Q ss_pred             EEEEEEEEEECCCCCEEEEEEEECCC------C--EEEEECCCC--CCCCCEE-----EEEECCCCCEEEEEEEECCCC-
Q ss_conf             99970579946898302699987568------5--499942788--7679749-----999955443769999930898-
Q gi|254780885|r   20 KVDLKGRFLLFDGTEYNCIVREISPG------G--LCIVCDVPM--FLVGERS-----IVFVEKVGRIEGKVVNFDSNR-   83 (207)
Q Consensus        20 ~v~l~GR~ll~d~~E~~C~t~diSpg------g--~~l~~~~~~--~~~Gerv-----v~Yld~iGrlEG~V~r~~~~~-   83 (207)
                      .+...|-.|+..   +||++++||..      -  +.+++ ..+  ++.-|-+     -.++-.+-|-|..+..+.+++ 
T Consensus        27 ~lrkgg~vvikg---rPCkVv~~stSKtGKHGhAK~~lvg-iDIFtgkk~ed~~Ps~hn~~vP~V~r~~yqli~I~dd~d  102 (166)
T PTZ00328         27 ALKKGGYVCING---RPCKVIDLSVSKTGKHGHAKVSIVA-TDIFTGNRLEDQAPSTHNVEVPFVKTFTYSVLDIQPNED  102 (166)
T ss_pred             CEEECCEEEECC---CCEEEEEEEECCCCCCCCCEEEEEE-EECCCCCEEEEEEECCCCCCCCEEECCEEEEEEECCCCC
T ss_conf             133889999888---5418999884679866630467898-861468666788605786225678802879986315666


Q ss_pred             ----CEEEEEECCHHHH
Q ss_conf             ----3899997698789
Q gi|254780885|r   84 ----GYAVRIVTSENER   96 (207)
Q Consensus        84 ----GFav~l~~t~~kR   96 (207)
                          ||.--+.-+..-|
T Consensus       103 ~~~~G~lsLm~e~G~~k  119 (166)
T PTZ00328        103 PSLPAHLSLMDDEGESR  119 (166)
T ss_pred             CCCCCEEEEECCCCCCC
T ss_conf             55541599996899823


No 38 
>pfam11356 Pilus_PilP Type IV pilus biogenesis. Type IV pili are required for auto-agglutination, twitching motility, biofilm formation, adherence and DNA uptake during transformation. PilP is an inner membrane protein, required for pilus expression and transformation. PilP interacts with PilQ which suggests that the two proteins may have coordinated activity in functions such as pilus extrusion/retraction.
Probab=23.87  E-value=56  Score=14.09  Aligned_cols=25  Identities=20%  Similarity=0.216  Sum_probs=15.0

Q ss_pred             EEEEECCCEEEECCCCCCCCCEEEE
Q ss_conf             9987424204551577899855897
Q gi|254780885|r  146 VIDISESGVSVSVDLQIEMFSKVLF  170 (207)
Q Consensus       146 iiDiS~SGAAi~~~~rp~iGs~V~v  170 (207)
                      |+-+.-.|-.+.+-.+.+-|..+.+
T Consensus        60 v~eI~G~~~~l~A~l~l~~G~~~dv   84 (108)
T pfam11356        60 VVEIFGRGGGLTATLRLPGGREVDV   84 (108)
T ss_pred             EEEEEEECCCEEEEEEECCCCEEEE
T ss_conf             9999803881899999189948986


No 39 
>cd04970 Ig6_Contactin_like Sixth Ig domain of contactin. Ig6_Contactin_like: Sixth Ig domain of contactins. Contactins are neural cell adhesion molecules and are comprised of six Ig domains followed by four fibronectin type III(FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. The first four Ig domains form the intermolecular binding fragment, which arranges as a compact U-shaped module via contacts between Ig domains 1 and 4, and between Ig domains 2 and 3. Contactin-2 (TAG-1, axonin-1) may play a part in the neuronal processes of neurite outgrowth, axon guidance and fasciculation, and neuronal migration. This group also includes contactin-1 and contactin-5. The different contactins show different expression patterns in the central nervous system. During development and in adulthood, contactin-2 is transiently expressed in subsets of central and peripheral neurons. Contactin-5 is expressed specifically in the rat postnatal nervous system, peaking at about 3 week
Probab=23.64  E-value=24  Score=16.30  Aligned_cols=46  Identities=13%  Similarity=0.115  Sum_probs=28.7

Q ss_pred             HHHHHCCCCCCCCHHCCCCC-CC---CCCCCCEEEEEECCCCEEEEEEEE
Q ss_conf             99876424367502102567-47---777651368995799889899998
Q gi|254780885|r  103 LIWLANKDDLHLQDCRAYGR-KI---TRDREVDAQLVLNDNTKHSCKVID  148 (207)
Q Consensus       103 LtWlanr~~l~l~e~R~h~R-~v---Pr~~~~~~~l~l~DG~~~~criiD  148 (207)
                      .+|+.|-+.+.+.++-.|-. ..   ..+.-....+++.|...|+|..-.
T Consensus        19 ~~W~~nG~~Id~~~~~~~~~~~~~~~~~gsL~I~n~~~~d~G~YtC~a~t   68 (85)
T cd04970          19 FTWSFNGVPIDFDKDGGHYRRVGGKDSNGDLMIRNAQLKHAGKYTCTAQT   68 (85)
T ss_pred             EEEEECCEEEECCCCCCCEEEEEECCCCCEEEEECCCHHCCCEEEEEEEC
T ss_conf             99978999952767776327873026576499931672119688999833


No 40 
>cd03079 GST_N_Metaxin2 GST_N family, Metaxin subfamily, Metaxin 2; a metaxin 1 binding protein identified through a yeast two-hybrid system using metaxin 1 as the bait. Metaxin 2 shares sequence similarity with metaxin 1 but does not contain a C-terminal mitochondrial outer membrane signal-anchor domain. It associates with mitochondrial membranes through its interaction with metaxin 1, which is a component of the mitochondrial preprotein import complex of the outer membrane. The biological function of metaxin 2 is unknown. It is likely that it also plays a role in protein translocation into the mitochondria. However, this has not been experimentally validated. In a recent proteomics study, it has been shown that metaxin 2 is overexpressed in response to lipopolysaccharide-induced liver injury.
Probab=23.39  E-value=31  Score=15.65  Aligned_cols=27  Identities=26%  Similarity=0.434  Sum_probs=19.5

Q ss_pred             EEEECCCCEEEEECCCCCCCCCEEEEEECCCC
Q ss_conf             99875685499942788767974999995544
Q gi|254780885|r   39 VREISPGGLCIVCDVPMFLVGERSIVFVEKVG   70 (207)
Q Consensus        39 t~diSpgg~~l~~~~~~~~~Gervv~Yld~iG   70 (207)
                      ..-|||+|     .+|.-++|..+++-|+.|=
T Consensus        42 AE~MSPsG-----kvPfi~~g~~vvaef~pIv   68 (74)
T cd03079          42 AEFMSPSG-----KVPFIRVGNQIVSEFGPIV   68 (74)
T ss_pred             CCCCCCCC-----CCCEEEECCEEEECHHHHH
T ss_conf             55118998-----7766875788561435798


No 41 
>PRK13616 lipoprotein LpqB; Provisional
Probab=22.38  E-value=44  Score=14.68  Aligned_cols=26  Identities=19%  Similarity=0.409  Sum_probs=17.7

Q ss_pred             EEEEEE----CCHHHHHHHHHHHHHHHCCC
Q ss_conf             899997----69878999999999876424
Q gi|254780885|r   85 YAVRIV----TSENERRKLADKLIWLANKD  110 (207)
Q Consensus        85 Fav~l~----~t~~kR~kLA~qLtWlanr~  110 (207)
                      ..+.|.    ++++.|.+||+||.|-.+..
T Consensus       250 ~~v~~~gl~~~~~~~r~~lAAQlvwTL~~a  279 (590)
T PRK13616        250 ARVDFTGLSTLDPHSRQLLAAQVVWTLARA  279 (590)
T ss_pred             CEEECCCCCCCCHHHHHHHHHHHEEECCCC
T ss_conf             156414777689999999887662322368


No 42 
>cd06497 ACD_alphaA-crystallin_HspB4 Alpha-crystallin domain found in the small heat shock protein (sHsp) alphaA-crystallin (HspB4, 20kDa). sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Alpha crystallin, an abundant protein in the mammalian lens, is a large (700 kDa) heteropolymer composed of HspB4 and HspB5, generally in a molar ratio of HspB4:HspB5 of 3:1.  Only trace amounts of HspB4 are found in tissues other than the lens. HspB5 does not belong to this group. Mutations inHspB4 have been associated with Autosomal Dominant Congenital Cataract (ADCC). The chaperone-like functions of HspB4 are considered important for maintaining lens transparency and preventing cataract.
Probab=22.02  E-value=60  Score=13.86  Aligned_cols=33  Identities=15%  Similarity=0.320  Sum_probs=15.2

Q ss_pred             EEEEEEEEEEECCCCCEEEEEEEECCCCEEEEE
Q ss_conf             799970579946898302699987568549994
Q gi|254780885|r   19 VKVDLKGRFLLFDGTEYNCIVREISPGGLCIVC   51 (207)
Q Consensus        19 V~v~l~GR~ll~d~~E~~C~t~diSpgg~~l~~   51 (207)
                      +.=+..=+|.||+.-+..-.+..+|..|+..+.
T Consensus        51 ~~r~F~R~~~LP~~vd~~~v~S~Ls~dG~L~I~   83 (86)
T cd06497          51 ISREFHRRYRLPSNVDQSAITCSLSADGMLTFS   83 (86)
T ss_pred             EEEEEEEEECCCCCCCHHHEEEEECCCCEEEEE
T ss_conf             999999976599998977979983899669998


No 43 
>pfam01356 A_amylase_inhib Alpha amylase inhibitor.
Probab=20.50  E-value=65  Score=13.67  Aligned_cols=18  Identities=28%  Similarity=0.486  Sum_probs=13.7

Q ss_pred             CEEEEEECCCCEEEEEEE
Q ss_conf             136899579988989999
Q gi|254780885|r  130 VDAQLVLNDNTKHSCKVI  147 (207)
Q Consensus       130 ~~~~l~l~DG~~~~crii  147 (207)
                      +..++.+.||...||+++
T Consensus        27 vsvtV~Y~dG~~~PCr~~   44 (68)
T pfam01356        27 VSVTVVYTDGTWGPCRTA   44 (68)
T ss_pred             EEEEEEEECCCCCEEEEE
T ss_conf             899999828971113771


No 44 
>cd04979 Ig_Semaphorin_C Immunoglobulin (Ig)-like domain of semaphorin. Ig_Semaphorin_C; Immunoglobulin (Ig)-like domain in semaphorins. Semaphorins are transmembrane protein that have important roles in a variety of tissues. Functionally, semaphorins were initially characterized for their importance in the development of the nervous system and in axonal guidance. Later they have been found to be important for the formation and functioning of the cardiovascular, endocrine, gastrointestinal, hepatic, immune, musculoskeletal, renal, reproductive, and respiratory systems. Semaphorins function through binding to their receptors and transmembrane semaphorins also serves as receptors themselves. Although molecular mechanism of semaphorins is poorly understood, the Ig-like domains may involve in ligand binding or dimerization.
Probab=20.40  E-value=18  Score=17.14  Aligned_cols=46  Identities=13%  Similarity=0.265  Sum_probs=27.6

Q ss_pred             HHHHHHHHCCCCCCCCHHCCCCCCCCCCC-CCEEEEEECCCCEEEEEE
Q ss_conf             99999876424367502102567477776-513689957998898999
Q gi|254780885|r  100 ADKLIWLANKDDLHLQDCRAYGRKITRDR-EVDAQLVLNDNTKHSCKV  146 (207)
Q Consensus       100 A~qLtWlanr~~l~l~e~R~h~R~vPr~~-~~~~~l~l~DG~~~~cri  146 (207)
                      -++.+|+.|++++.-.+ +.+.|+..... -....+..+|...|.|.-
T Consensus        24 ~A~V~W~~ng~~l~~~~-~~~~r~~~~~~gLlI~~v~~~daG~Y~C~a   70 (89)
T cd04979          24 LASVVWLFQGGPLQRKE-EPEERLLVTEDGLLIRSVSPADAGVYTCQS   70 (89)
T ss_pred             CCEEEEEECCCCCCCCC-CCCCEEEECCCCEEEECCCHHHCEEEEEEE
T ss_conf             85389998995377655-666228953784799227942197999998


No 45 
>cd07703 Ig2_Nectin-2_like Second immunoglobulin (Ig) domain of nectin-2 (also known as poliovirus receptor related protein 2 or CD112) and similar proteins. Ig2_Nectin-2_like: domain similar to the second immunoglobulin (Ig) domain of nectin-2 (also known as poliovirus receptor related protein 2 or CD112). Nectin-2 belongs to the nectin family comprised of four transmembrane glycoproteins (nectins-1 through 4). Nectins are synaptic cell adhesion molecules (CAMs) which facilitate adhesion and signaling at various intracellular junctions. Nectins form homophilic cis-dimers, followed by homophilic and heterophilic trans-dimers involved in cell-cell adhesion.  Nectin-2 and nectin-3 localize at Sertoli-spermatid junctions where they form heterophilic trans-interactions between the cells that are essential for the formation and maintenance of the junctions and for spermatid development.
Probab=20.13  E-value=50  Score=14.39  Aligned_cols=52  Identities=12%  Similarity=0.150  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHCCCCCCCCHHCCCCCCCCCCCCCEEEEEE-----CCCCEEEEEEEEEEC
Q ss_conf             9999999987642436750210256747777651368995-----799889899998742
Q gi|254780885|r   97 RKLADKLIWLANKDDLHLQDCRAYGRKITRDREVDAQLVL-----NDNTKHSCKVIDISE  151 (207)
Q Consensus        97 ~kLA~qLtWlanr~~l~l~e~R~h~R~vPr~~~~~~~l~l-----~DG~~~~criiDiS~  151 (207)
                      .|=+++++|.-+  ..+..+-.. ..-.+..-.+.|+++|     .||..++|.+--=|+
T Consensus        27 grP~A~IsW~s~--l~g~~~~~~-~~~~~gT~TV~S~~~lvPs~~~~G~~vtCvV~H~sl   83 (95)
T cd07703          27 GRPPARISWSST--LGGNANTTS-KENGDGTVTVTSEYSLVPTPEANGKEVTCKVEHETL   83 (95)
T ss_pred             CCCCCEEEEECC--CCCCCCEEE-ECCCCCCEEEEEEEEEEECHHHCCCEEEEEEECCCC
T ss_conf             919954387868--899742576-458999899999999976857889685999856876


No 46 
>smart00783 A_amylase_inhib Alpha amylase inhibitor. Alpha amylase inhibitor inhibits mammalian alpha-amylases specifically, by forming a tight stoichiometric 1:1 complex with alpha-amylase. The inhibitor has no action on plant and microbial alpha amylases.
Probab=20.09  E-value=66  Score=13.61  Aligned_cols=18  Identities=28%  Similarity=0.486  Sum_probs=13.7

Q ss_pred             CEEEEEECCCCEEEEEEE
Q ss_conf             136899579988989999
Q gi|254780885|r  130 VDAQLVLNDNTKHSCKVI  147 (207)
Q Consensus       130 ~~~~l~l~DG~~~~crii  147 (207)
                      +..++.+.||...||+++
T Consensus        28 vsVtV~Y~dG~~~PCr~~   45 (69)
T smart00783       28 VSVTVVYTDGTWGPCRTA   45 (69)
T ss_pred             EEEEEEEECCCCCEEEEE
T ss_conf             899999828971113771


Done!