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!