Query 028781
Match_columns 204
No_of_seqs 144 out of 363
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 02:26:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028781.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028781hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3285 Spindle assembly check 100.0 6.2E-51 1.3E-55 326.0 15.1 185 7-197 9-200 (203)
2 KOG3186 Mitotic spindle checkp 100.0 4.8E-49 1E-53 313.7 15.4 189 12-200 5-201 (202)
3 PF02301 HORMA: HORMA domain; 100.0 1.8E-33 3.8E-38 233.6 20.6 176 9-188 1-208 (208)
4 KOG4652 HORMA domain [Chromati 99.5 3.8E-13 8.2E-18 117.2 12.7 182 9-192 8-215 (324)
5 PF07855 DUF1649: Protein of u 98.4 7.2E-06 1.6E-10 66.3 13.2 124 14-138 7-159 (163)
6 PF10033 ATG13: Autophagy-rela 94.3 0.46 1E-05 40.4 9.8 124 17-149 1-180 (233)
7 KOG4493 Uncharacterized conser 90.1 4.1 8.8E-05 34.2 9.8 129 17-145 17-178 (219)
8 PF06581 p31comet: Mad1 and Cd 85.1 12 0.00027 32.5 10.0 120 7-131 54-189 (264)
9 KOG3874 Uncharacterized conser 61.1 1E+02 0.0022 28.7 9.9 84 46-134 51-136 (504)
10 TIGR02241 conserved hypothetic 42.7 84 0.0018 24.4 5.8 46 51-100 62-107 (140)
11 PF06327 DUF1053: Domain of Un 40.2 47 0.001 24.1 3.8 38 52-89 50-88 (101)
12 PF14242 DUF4342: Domain of un 38.9 39 0.00084 24.3 3.0 28 56-83 9-36 (84)
13 PF13103 TonB_2: TonB C termin 37.4 1.3E+02 0.0029 20.4 6.9 73 60-145 3-82 (85)
14 PF09754 PAC2: PAC2 family; I 37.1 26 0.00057 28.7 2.2 50 35-84 56-105 (219)
15 PF06841 Phage_T4_gp19: T4-lik 34.0 1.5E+02 0.0033 22.1 5.9 46 51-100 58-103 (134)
16 cd02969 PRX_like1 Peroxiredoxi 29.0 80 0.0017 24.6 3.7 58 82-140 112-169 (171)
17 PF09652 Cas_VVA1548: Putative 27.7 36 0.00078 25.1 1.3 14 51-64 2-15 (93)
18 PF10259 Rogdi_lz: Rogdi leuci 26.2 4.2E+02 0.0091 22.9 8.0 85 57-168 91-199 (273)
19 PF02603 Hpr_kinase_N: HPr Ser 26.2 13 0.00028 28.5 -1.3 51 7-57 64-115 (127)
20 PF09457 RBD-FIP: FIP domain ; 24.3 40 0.00086 21.8 0.9 18 53-70 21-38 (48)
21 PF09954 DUF2188: Uncharacteri 23.8 1.6E+02 0.0035 19.3 3.9 33 64-98 30-62 (62)
22 KOG3744 Uncharacterized conser 23.8 80 0.0017 27.5 2.9 30 1-30 77-106 (311)
23 PRK05428 HPr kinase/phosphoryl 22.2 98 0.0021 27.6 3.3 80 7-87 65-146 (308)
24 PRK14133 DNA polymerase IV; Pr 20.8 5.8E+02 0.013 22.4 9.4 83 36-126 236-320 (347)
No 1
>KOG3285 consensus Spindle assembly checkpoint protein [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=100.00 E-value=6.2e-51 Score=325.97 Aligned_cols=185 Identities=19% Similarity=0.396 Sum_probs=171.4
Q ss_pred CCChHHHHHHHHHHHHHHHHHhhhccCCCCCcccceeeeccceeeeccChhHHHHHHHHHHHHHHHHHcCCccEEEEEEE
Q 028781 7 QSPQVETARILAEFLEVAITSVVFLKGLYPSGAFERRRYMNLVVQRARHPQLRDYIHSSVSSLLLFIQKGLVERVAVIFS 86 (204)
Q Consensus 7 ~~~~~~s~~~v~efLevaih~ILY~R~vYP~~~F~~~r~ynl~v~~sr~p~l~~YI~~~l~~v~~~L~~g~l~kl~lvI~ 86 (204)
.+|+.+|+.+|.|||+++||+|||+|||||+|+|.++|+||++++++.+++|+.||++++.|+.+||.+|+++|+++||.
T Consensus 9 ~isLkGSa~iV~EFf~y~iNSILyQRgiYPaEdF~~vkKYgLtllvs~D~elk~f~~~ilsQ~~~WL~~~kiqklvlvI~ 88 (203)
T KOG3285|consen 9 CISLKGSAQIVSEFFEYGINSILYQRGIYPAEDFVRVKKYGLTLLVSHDEELKTFIRNILSQVHEWLSKGKIQKLVLVIT 88 (203)
T ss_pred eeEeechHHHHHHHHHhhhhHHHHhccCCcHHHhhHHHhcCceEEEecCHHHHHHHHHHHHHHHHHHHhCCcceEEEEEE
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCC-CceeeEEEEeeeeccCCC------CCCChhHHHHHHHHHHHHHHhhcccCCCCCCCeeEEEEEEEeeCCCCCCCCC
Q 028781 87 NAN-NVPLERYVFKIMVNQSYG------SMVEEGHLEFSLRSFLIKLSVSKSLSKVLPQGCRWEITAYFCSLPQVNTSKD 159 (204)
Q Consensus 87 ~~~-~~~lEr~~Fdi~~~~~~~------~~~~~~~ie~~~ra~L~~l~~~~~~Lp~l~~~~tF~i~v~~~~~~~~~~~~~ 159 (204)
++. |+++|||+||++.....+ ...++..++.+||++||||+++++|||.|.+.|+|++++||+. +.+.
T Consensus 89 ~~~tgEvlErWqFnie~~~~~~d~~na~~~k~~~~iq~EIraviRQItasVtfLP~Le~~ctFdvLiyTdk-----D~~v 163 (203)
T KOG3285|consen 89 SKHTGEVLERWQFNIETENTASDGQNATRVKDLKRIQNEIRAVIRQITASVTFLPLLEEICTFDVLIYTDK-----DTEV 163 (203)
T ss_pred ecccccchhheeeeeeeeccccCcccccchhHHHHHHHHHHHHHHHHhhheeecccccceeEEEEEEEeCC-----CccC
Confidence 998 899999999999875432 2346778999999999999999999999999999999999953 3457
Q ss_pred CCCceecCccCcCCCCceeeeeEeecCceEEEEEEeec
Q 028781 160 AELWIPTDTKQWQQPPLITPIKSMSSDSLSVQLYLENP 197 (204)
Q Consensus 160 ~~~Wi~~d~~~~~~~~~~~pl~sv~~~~l~~~~~vE~~ 197 (204)
|..|+.++++. .++++.+.+||++++.+++++-+-+.
T Consensus 164 P~~W~eS~~~~-I~n~e~VqlrsFsT~~HKVdt~V~YK 200 (203)
T KOG3285|consen 164 PEKWDESGPKL-IQNPEAVQLRSFSTSIHKVDTQVSYK 200 (203)
T ss_pred CcchhcCCCeE-ecChhhEEEeeccccceeecceEEec
Confidence 89999999987 57889999999999999999988664
No 2
>KOG3186 consensus Mitotic spindle checkpoint protein [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=4.8e-49 Score=313.71 Aligned_cols=189 Identities=23% Similarity=0.344 Sum_probs=172.4
Q ss_pred HHHHHHHHHHHHHHHHhhhccCCCCCcccceeeeccceeeeccChhHHHHHHHHHHHHHHHHHcCCccEEEEEEECCCCc
Q 028781 12 ETARILAEFLEVAITSVVFLKGLYPSGAFERRRYMNLVVQRARHPQLRDYIHSSVSSLLLFIQKGLVERVAVIFSNANNV 91 (204)
Q Consensus 12 ~s~~~v~efLevaih~ILY~R~vYP~~~F~~~r~ynl~v~~sr~p~l~~YI~~~l~~v~~~L~~g~l~kl~lvI~~~~~~ 91 (204)
..+++++||++|++|+|||.|++||.++|.++|+||.||++||||.||+||.+++++++++|++|.|++++|+|++|+++
T Consensus 5 ~~ad~~~e~meV~Vh~ILYvR~~YP~~iF~k~rkYN~pv~~S~hP~Ln~Yi~~vl~s~~elL~~~~v~~v~l~i~~KE~r 84 (202)
T KOG3186|consen 5 ENADGWSEKMEVSVHCILYVRRLYPQDIFIKARKYNTPVWQSRHPILNEYIEEVLQSCIELLQTGSVHQVALSIINKEQR 84 (202)
T ss_pred ecchHHHHHHHHHHHhheeecccccHHHHHHHHhcCCceeeecCchHHHHHHHHHHHHHHHHhcCCeeEEEEEEEccccC
Confidence 35789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeEEEEeeeeccCCCCCC--ChhHHHHHHHHHHHHHHhhcccCCCCCCC-eeEEEEEEEeeCCCCCCCC----CCCCce
Q 028781 92 PLERYVFKIMVNQSYGSMV--EEGHLEFSLRSFLIKLSVSKSLSKVLPQG-CRWEITAYFCSLPQVNTSK----DAELWI 164 (204)
Q Consensus 92 ~lEr~~Fdi~~~~~~~~~~--~~~~ie~~~ra~L~~l~~~~~~Lp~l~~~-~tF~i~v~~~~~~~~~~~~----~~~~Wi 164 (204)
++|||+|.++..+...+.. -..+.++-+||+|.||+.+...||.+|.+ |||+++++|++.+..+.++ .||||+
T Consensus 85 ~~E~yvf~~~s~p~~~~~~d~~l~~~eq~mRa~i~kis~~~n~lp~~p~G~Ctftv~vht~~~a~r~~~~~~~~~~FPw~ 164 (202)
T KOG3186|consen 85 EEERYVFSTDSIPIIPDFLDEFLDAYEQYMRASIIKISNITNGLPLIPQGICTFTVRVHTKDGAPRPKQWEEWFLPFPWA 164 (202)
T ss_pred hhhheEeeccCCCcCchhHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCceeEEEEEEEeccccccCcchHHhhcCCchh
Confidence 9999999998877654322 35689999999999999999999999988 9999999999998887653 589999
Q ss_pred ecCcc-CcCCCCceeeeeEeecCceEEEEEEeecCCc
Q 028781 165 PTDTK-QWQQPPLITPIKSMSSDSLSVQLYLENPSLL 200 (204)
Q Consensus 165 ~~d~~-~~~~~~~~~pl~sv~~~~l~~~~~vE~~~~~ 200 (204)
.++.. .+...+.++|+|.||.|+|+|++|+|+..-|
T Consensus 165 ~~~~~~~q~~gv~liPl~~vd~~~lkm~i~ve~~~~~ 201 (202)
T KOG3186|consen 165 RETDATRQFKGVILIPLRNVDIGPLKMEIWVEKYTNS 201 (202)
T ss_pred hcchhhhhccCcEEEeeeecccCceEEEEEEEeeccC
Confidence 99864 3556679999999999999999999997654
No 3
>PF02301 HORMA: HORMA domain; InterPro: IPR003511 The HORMA (for Hop1p, Rev7p and MAD2) domain has been suggested to recognise chromatin states that result from DNA adducts, double stranded breaks or non-attachment to the spindle and acts as an adaptor that recruits other proteins. Hop1 is a meiosis-specific protein, Rev7 is required for DNA damage induced mutagenesis, and MAD2 is a spindle checkpoint protein which prevents progression of the cell cycle upon detection of a defect in mitotic spindle integrity [, ].; GO: 0007067 mitosis; PDB: 3ABD_B 3ABE_C 4AEZ_H 2V64_A 2VFX_A 1GO4_D 2QYF_C 3GMH_B 1KLQ_A 1S2H_A ....
Probab=100.00 E-value=1.8e-33 Score=233.62 Aligned_cols=176 Identities=27% Similarity=0.420 Sum_probs=138.9
Q ss_pred ChHHHHHHHHHHHHHHHHHhhhccCCCCCcccceeeecccee------eeccChhHHHHHHHHHHHHHHHHHcCCccEEE
Q 028781 9 PQVETARILAEFLEVAITSVVFLKGLYPSGAFERRRYMNLVV------QRARHPQLRDYIHSSVSSLLLFIQKGLVERVA 82 (204)
Q Consensus 9 ~~~~s~~~v~efLevaih~ILY~R~vYP~~~F~~~r~ynl~v------~~sr~p~l~~YI~~~l~~v~~~L~~g~l~kl~ 82 (204)
|.++|+.++++||++|||+|||+|||||++.|++++.||+.+ +.+|||.|++||++ ++.++|.+|.|++|+
T Consensus 1 t~~qS~~~v~~~L~~~is~Ily~R~lyP~~~F~~~~~~~~~~k~l~~~~~~~~~~l~~~i~~---~v~dai~k~~L~~v~ 77 (208)
T PF02301_consen 1 TEQQSLELVKEFLEVAISQILYLRGLYPEDCFEDRRFYGLKLKVLVPNYSSRAPQLIDYIEK---GVFDAIEKGYLKKVV 77 (208)
T ss_dssp EHHHHHHHHHHHHHHHHHHHHHHTTSS-GGGEEEEEETTEEE-----TEEE--HHHHHHHHH---HHHHHHHTTSEEEEE
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhccCCHHHCcEEEecCccccccccccCCCcHHHHHHHHh---hHHHHHhhCcceEEE
Confidence 578999999999999999999999999999999999999888 79999999999988 899999999999999
Q ss_pred EEEECC----CCceeeEEEEeeeeccCCC------------------CCCChhHHHHHHHHHHHHHHhhcccCCCCCCCe
Q 028781 83 VIFSNA----NNVPLERYVFKIMVNQSYG------------------SMVEEGHLEFSLRSFLIKLSVSKSLSKVLPQGC 140 (204)
Q Consensus 83 lvI~~~----~~~~lEr~~Fdi~~~~~~~------------------~~~~~~~ie~~~ra~L~~l~~~~~~Lp~l~~~~ 140 (204)
|+|++. +++++|||+|+|++.+..+ +..++.+++.++|++|++|..+.+.||+||++|
T Consensus 78 l~I~~~d~~~~~~~lE~y~F~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lr~l~~~~~~L~~LP~~~ 157 (208)
T PF02301_consen 78 LVIYDDDPPKSNEVLERYTFSFSYFPDGGPMSPEGSSISISNNTSEIDPITLDEVQEQLRALLRKLISSTQSLPPLPDER 157 (208)
T ss_dssp EEEE----ETTTCEEEEEEEEEEE-TTGGGTSSC----------HHHCSSCHHHHHHHHHHHHHHHHHHHCTSSS--TTS
T ss_pred EEEEecccCCCCceeEEEEEEEEecCCCCcccccccccccccccccccCCCHHHHHHHHHHHHHHHHHHhccCCCccCCc
Confidence 999964 4789999999999964321 135789999999999999999999999999998
Q ss_pred eEEEEEEEeeCCCCCCCC-CCCCceecCcc---CcCCCCceeeeeEeecCce
Q 028781 141 RWEITAYFCSLPQVNTSK-DAELWIPTDTK---QWQQPPLITPIKSMSSDSL 188 (204)
Q Consensus 141 tF~i~v~~~~~~~~~~~~-~~~~Wi~~d~~---~~~~~~~~~pl~sv~~~~l 188 (204)
++++.+++.++. .+..+ ..+.|...... .+...+..+++++|+||.|
T Consensus 158 ~~~~~l~~~~~t-p~dy~pp~f~~~~~~~~~~~~~~~~~~~~~vg~v~t~~H 208 (208)
T PF02301_consen 158 TLTFKLLYYDDT-PEDYEPPGFEAAEEATSFPLIFDEEPERVSVGSVSTGHH 208 (208)
T ss_dssp SEEEEEEEEES--ETTSCSST-TEEES--STEEESSCSEEEEEEEEEEESSE
T ss_pred eEEEEEEEEeCC-CccccCCCCCCcccccccccccccceEEEEEeeeeCCCC
Confidence 777777666542 12222 12345554211 2456679999999999975
No 4
>KOG4652 consensus HORMA domain [Chromatin structure and dynamics]
Probab=99.49 E-value=3.8e-13 Score=117.16 Aligned_cols=182 Identities=16% Similarity=0.253 Sum_probs=138.8
Q ss_pred ChHHHHHHHHHHHHHHHHHhhhccCCCCCcccceeeecc--cee-eeccChhHHH-HHHHHHHHHHHHHHcCCccEEEEE
Q 028781 9 PQVETARILAEFLEVAITSVVFLKGLYPSGAFERRRYMN--LVV-QRARHPQLRD-YIHSSVSSLLLFIQKGLVERVAVI 84 (204)
Q Consensus 9 ~~~~s~~~v~efLevaih~ILY~R~vYP~~~F~~~r~yn--l~v-~~sr~p~l~~-YI~~~l~~v~~~L~~g~l~kl~lv 84 (204)
...+|..++++.|.+||..|||.|||+|++.|..+.-.+ +.+ ...+.|.=.. -|...+..+.+.+..|.+++++++
T Consensus 8 ~e~~Sl~f~~rll~~ais~Ilr~Rgi~pe~yf~~~~v~~~~l~~~~~~~~~a~~~~li~~l~kg~~dai~~k~Lk~lslv 87 (324)
T KOG4652|consen 8 NEKQSLEFMTRLLYVAISTILRERGIFPEEYFKDRYVDGNLLVMTLLRRQDAPEGRLVSWLEKGVHDAIRQKLLKKLSLV 87 (324)
T ss_pred cchhHHHHHHHHHHHHHHHHHHhcccchHHhcccccccchhhhhhhhccCCccccchHHHHHHHHHHHHHHHHHhheEEE
Confidence 467899999999999999999999999999999999877 444 3333333221 255666777888999999999999
Q ss_pred EECCC-CceeeEEEEeeeeccCCC-------------C------CCChhHHHHHHHHHHHHHHhhcccCCCCCCCeeEEE
Q 028781 85 FSNAN-NVPLERYVFKIMVNQSYG-------------S------MVEEGHLEFSLRSFLIKLSVSKSLSKVLPQGCRWEI 144 (204)
Q Consensus 85 I~~~~-~~~lEr~~Fdi~~~~~~~-------------~------~~~~~~ie~~~ra~L~~l~~~~~~Lp~l~~~~tF~i 144 (204)
|.+++ .+.+|-|+|.|.|+..++ + ....++..+++..+++++.-+...|.|||+.|.-.+
T Consensus 88 i~~~~d~~~IE~yifsF~Y~e~g~v~~~in~~~n~~s~~~~e~s~l~~ddtrr~~~~lir~~~i~~q~LePLP~~~~~~~ 167 (324)
T KOG4652|consen 88 ITESEDPEDIEVYIFSFVYDEEGSVSARINYGINGQSSKAFELSQLSMDDTRRQFAKLIRKLHICTQLLEPLPQGLILSM 167 (324)
T ss_pred EecCCCCcceeEEEEEEEecCCCceeEEEecCCCCCcCchhhhhhhhhHHHHHHHHHHHHHHHHHHHhccCccchhhhhh
Confidence 99988 678899999999986531 1 123446899999999999999999999999988888
Q ss_pred EEEEeeCCCCCCCCCCCCceecCcc--CcCCCCceeeeeEeecCceEEEE
Q 028781 145 TAYFCSLPQVNTSKDAELWIPTDTK--QWQQPPLITPIKSMSSDSLSVQL 192 (204)
Q Consensus 145 ~v~~~~~~~~~~~~~~~~Wi~~d~~--~~~~~~~~~pl~sv~~~~l~~~~ 192 (204)
.+|..+.+. +.. +|.-.-.+++. .+...+.-.-|+.++++.+++.+
T Consensus 168 rl~Y~e~~p-pDy-qP~gFkd~~~~~y~~p~~p~~~~IG~v~~~hH~~~~ 215 (324)
T KOG4652|consen 168 RLYYTERVP-PDY-QPEGFKDSTRAFYTLPVNPEQINIGAVSTPHHKGFV 215 (324)
T ss_pred eeeecccCC-ccC-CCcccccCccceeecCCCccceeeccccCccceeEE
Confidence 888755432 233 35545555422 22445666889999999887766
No 5
>PF07855 DUF1649: Protein of unknown function (DUF1649); InterPro: IPR012445 This family represents Autophagy-related protein 101.
Probab=98.44 E-value=7.2e-06 Score=66.33 Aligned_cols=124 Identities=15% Similarity=0.277 Sum_probs=94.3
Q ss_pred HHHHHHHHHHHHHHhhhccCCCCCcccc--eeeeccceeeeccChhHHHHHHHHHHHHHHHHHcCCcc--------EEEE
Q 028781 14 ARILAEFLEVAITSVVFLKGLYPSGAFE--RRRYMNLVVQRARHPQLRDYIHSSVSSLLLFIQKGLVE--------RVAV 83 (204)
Q Consensus 14 ~~~v~efLevaih~ILY~R~vYP~~~F~--~~r~ynl~v~~sr~p~l~~YI~~~l~~v~~~L~~g~l~--------kl~l 83 (204)
...+.|-+...+|+|||+|-+ +.=.-. ..-.+|+....+.+|+|..-|++-++++..++.++.-. +|+|
T Consensus 7 ~~~v~evv~~ilHTIlFhR~~-G~v~p~dv~~e~ldiTy~~~~~~el~~~Id~ki~~f~~~l~~~~~~~~~~~~~gqI~l 85 (163)
T PF07855_consen 7 RSQVREVVKAILHTILFHRAF-GTVRPKDVTCEFLDITYPRCNDPELESLIDEKINQFIRQLEKHPSKSSNGLGRGQISL 85 (163)
T ss_pred HHHHHHHHHHHHHHHHhhhcc-CcccccccccceecceeeccCcHHHHHHHHHHHHHHHHHHHhCcCccCCCcceEEEEE
Confidence 356889999999999999933 333333 33457888888999999999999999999999877655 8888
Q ss_pred EEECCC------------CceeeEEEEeeeeccCCCC---CCChhHHHHHHHHHHHHHHhhcc----cCCCCCC
Q 028781 84 IFSNAN------------NVPLERYVFKIMVNQSYGS---MVEEGHLEFSLRSFLIKLSVSKS----LSKVLPQ 138 (204)
Q Consensus 84 vI~~~~------------~~~lEr~~Fdi~~~~~~~~---~~~~~~ie~~~ra~L~~l~~~~~----~Lp~l~~ 138 (204)
.++.+. ..+.|+|+.++...+..+. ......+.++|+..+.+|...+. .+||++.
T Consensus 86 ~F~ekr~kk~WF~~~~~e~v~WE~W~I~v~v~~~~~~~er~~~r~~~~~~L~~~l~~Ii~~vn~~kdhIPpIts 159 (163)
T PF07855_consen 86 QFYEKRRKKSWFVGSGEEEVPWEQWTINVTVATPRTESERQKVREAVEDSLREALFKIIEIVNRHKDHIPPITS 159 (163)
T ss_pred EEEeecccccccccCCcccccceEEEEEEEEEcCCCchHHHHHHHHHHHHHHHHHHHHHHHHCcCcccCCCCCC
Confidence 888643 2488999999988754322 12334688899999999987654 6677754
No 6
>PF10033 ATG13: Autophagy-related protein 13; InterPro: IPR018731 Members of this family of phosphoproteins are involved in cytoplasm to vacuole transport (Cvt), and more specifically in Cvt vesicle formation. They are probably involved in the switching machinery regulating the conversion between the Cvt pathway and autophagy. Finally, ATG13 is also required for glycogen storage [, , ].
Probab=94.35 E-value=0.46 Score=40.40 Aligned_cols=124 Identities=15% Similarity=0.137 Sum_probs=76.7
Q ss_pred HHHHHHHHHHHhhhccC--------CCCCcccceee-eccceeeeccChhHHHHHHHHHHHHHHHHHcCCc----cEEEE
Q 028781 17 LAEFLEVAITSVVFLKG--------LYPSGAFERRR-YMNLVVQRARHPQLRDYIHSSVSSLLLFIQKGLV----ERVAV 83 (204)
Q Consensus 17 v~efLevaih~ILY~R~--------vYP~~~F~~~r-~ynl~v~~sr~p~l~~YI~~~l~~v~~~L~~g~l----~kl~l 83 (204)
|.+|+.-+.+.|+--|- ......+.+.- -||+-+ -..|.+.+ .++.|...+.. .-+++
T Consensus 1 I~~F~~Kaa~iIl~SR~~~~~~~~~~~~~~~~~~~nkWFNL~~--~e~~~~~~-------~l~~w~~~~~~~~~~pPlvI 71 (233)
T PF10033_consen 1 IQNFFLKAAQIILQSRLNLSPSSSSSSSSSSSRKRNKWFNLEI--DESDELRE-------ELKRWRSCSDLESRLPPLVI 71 (233)
T ss_pred ChHHHHHHHHHheeeccccCCCcccccccCCCCCCCccEeecC--CCcHHHHH-------HHHHhhhcccccCCCCCEEE
Confidence 46899999999999998 22233343333 499886 55555554 44556653332 23444
Q ss_pred EEE-CC----------------------------CCceeeEEEEeeeeccC----CCCCCChhHHHHHHHHHHHHHHhhc
Q 028781 84 IFS-NA----------------------------NNVPLERYVFKIMVNQS----YGSMVEEGHLEFSLRSFLIKLSVSK 130 (204)
Q Consensus 84 vI~-~~----------------------------~~~~lEr~~Fdi~~~~~----~~~~~~~~~ie~~~ra~L~~l~~~~ 130 (204)
-|+ +. .+.++|||++.++..+. .+.......+++.+-=.+|.|-+.+
T Consensus 72 ei~Ld~~~l~~~~~l~l~d~~g~~~~v~~~~~~~~~ivLERW~i~~~~~~~~~~~~~~~~~l~~vYK~~ivLfRSLys~~ 151 (233)
T PF10033_consen 72 EIYLDTRQLSSNQSLVLKDDDGKRWDVCKGRSKKSEIVLERWLIELDSSSSPPSPSDSGPELPTVYKRSIVLFRSLYSLT 151 (233)
T ss_pred EEEEecCCCCCCCceEecCCCCceeeecccccCCCcEEEEEEEEEEecCCCCCCccccchhHHHHHHHHHHHHHHHHHHH
Confidence 443 11 14589999999982111 1223456789999999999998888
Q ss_pred ccCCCC----------CCCeeEEEEEEEe
Q 028781 131 SLSKVL----------PQGCRWEITAYFC 149 (204)
Q Consensus 131 ~~Lp~l----------~~~~tF~i~v~~~ 149 (204)
..||.- -....|+|.....
T Consensus 152 RlLPA~kl~~~l~~~~~~~~~l~i~~Ri~ 180 (233)
T PF10033_consen 152 RLLPAYKLFRRLAKSSSSSSSLSIGYRIS 180 (233)
T ss_pred HhChHHHHHHHhhhccCCCCcceeEEEEe
Confidence 888742 1235677665443
No 7
>KOG4493 consensus Uncharacterized conserved protein [Function unknown]
Probab=90.13 E-value=4.1 Score=34.22 Aligned_cols=129 Identities=12% Similarity=0.248 Sum_probs=83.5
Q ss_pred HHHHHHHHHHHhhhccCC----CCCc---ccceee-------eccceeeeccChhHHHHHHHHHHHHHHHHHcCC---cc
Q 028781 17 LAEFLEVAITSVVFLKGL----YPSG---AFERRR-------YMNLVVQRARHPQLRDYIHSSVSSLLLFIQKGL---VE 79 (204)
Q Consensus 17 v~efLevaih~ILY~R~v----YP~~---~F~~~r-------~ynl~v~~sr~p~l~~YI~~~l~~v~~~L~~g~---l~ 79 (204)
+.|-..+.+|++||+|.+ |-.+ +|.... .+++....+...+|+.=|+..+.+.++||++.. +.
T Consensus 17 v~eaV~~ifh~vLlhR~vgkf~y~~~~~~s~GtVg~kdvdce~iDiTYV~~~s~EL~~kl~~~i~qF~~~ir~~~~~g~g 96 (219)
T KOG4493|consen 17 VTEAVTCIFHTVLLHREVGKFVYGVELHRSFGTVGAKDVDCEFIDITYVRCVSAELNEKLDEKIAQFIDTIRNEAGAGVG 96 (219)
T ss_pred cchhhhhHHHHHHHHHhhhheEecceeEEEeccccccccceeEEEEEEEEechHHHHHHHHHHHHHHHHHHHhCCCCCcc
Confidence 567788899999999986 2222 222222 134444567788899999999999999998654 56
Q ss_pred EEEEEEECCC----------CceeeEEEEeeeeccCCC---CCCChhHHHHHHHHHHHHH---HhhcccCCCCCCCeeEE
Q 028781 80 RVAVIFSNAN----------NVPLERYVFKIMVNQSYG---SMVEEGHLEFSLRSFLIKL---SVSKSLSKVLPQGCRWE 143 (204)
Q Consensus 80 kl~lvI~~~~----------~~~lEr~~Fdi~~~~~~~---~~~~~~~ie~~~ra~L~~l---~~~~~~Lp~l~~~~tF~ 143 (204)
.+.|-+|.+. +-|.|.|...++.....+ ......++-+-+-+-..+| ...-+++|..|....|.
T Consensus 97 Qi~L~FYekskK~~Wf~~~e~ipWEqW~l~l~vl~~~~~~e~q~~rs~vs~~l~ekv~~i~E~~Nr~~y~pk~ptq~e~~ 176 (219)
T KOG4493|consen 97 QISLEFYEKSKKKRWFFKDETIPWEQWTLHLDVLEEESEDERQYCRSHVSDLLEEKVEQIVEAMNRRSYLPKMPTQSESD 176 (219)
T ss_pred eEeeeeeecccCCCCCcCCCCccceeEEEEEEEeecccccccHHHHHHHHHHHHHHHHHHHHHhhhhccCcCCchhhhcc
Confidence 7999999872 358999999988875421 2222222333333333333 33445778777766655
Q ss_pred EE
Q 028781 144 IT 145 (204)
Q Consensus 144 i~ 145 (204)
..
T Consensus 177 ~i 178 (219)
T KOG4493|consen 177 NI 178 (219)
T ss_pred hh
Confidence 43
No 8
>PF06581 p31comet: Mad1 and Cdc20-bound-Mad2 binding; InterPro: IPR009511 This entry represents Mad1 and Cdc20-bound-Mad2 binding proteins that are involved in the cell-cycle surveillance mechanism called the spindle checkpoint []. This mechanism monitors the proper bipolar attachment of sister chromatids to spindle microtubules and ensures the fidelity of chromosome segregation during mitosis. A key player in mitosis is Mad2, which exhibits an unusual two-state behaviour. A Mad1-Mad2 core complex recruits cytosolic Mad2 to kinetochores through Mad2 dimerisation and converts Mad2 to a conformer amenable to Cdc20 binding. p31comet inactivates the checkpoint by binding to Mad1- or Cdc20-bound Mad2 in such a way as to stop Mad2 activation and to promote the dissociation of the Mad2-Cdc20 complex [].; GO: 0007096 regulation of exit from mitosis, 0005634 nucleus; PDB: 2QYF_B.
Probab=85.09 E-value=12 Score=32.49 Aligned_cols=120 Identities=18% Similarity=0.204 Sum_probs=56.8
Q ss_pred CCChHHHHHHHHHHHHHHHHHhhhccCCCCCc----c-cceeeec--cc---eeeeccChh------HHHHHHHHHHHHH
Q 028781 7 QSPQVETARILAEFLEVAITSVVFLKGLYPSG----A-FERRRYM--NL---VVQRARHPQ------LRDYIHSSVSSLL 70 (204)
Q Consensus 7 ~~~~~~s~~~v~efLevaih~ILY~R~vYP~~----~-F~~~r~y--nl---~v~~sr~p~------l~~YI~~~l~~v~ 70 (204)
-+|++....+++|+|+ .|||+|+=-|-. . |.++..- .. .+..+.+-. +-+=+++++..+.
T Consensus 54 ~vtqd~ccrfV~ElLK----~iLYQRqQiPlpYeQL~~f~~k~pq~~d~~~kk~~~~~~~~~kKcqq~L~eLE~vl~hLe 129 (264)
T PF06581_consen 54 PVTQDGCCRFVCELLK----HILYQRQQIPLPYEQLAFFYRKSPQAKDDVRKKVSFSTEQSNKKCQQALQELESVLSHLE 129 (264)
T ss_dssp ---HHHHHHHHHHHHH----HHHHHTTSSSS-HHHHT-----------------------HHHHHHHHHHHHHHHHHHHH
T ss_pred ccccchhHHHHHHHHH----HHHhhhhcCCChHHHHHHHHhcCcccccccccccccccchhhHHHHHHHHHHHHHHHHHH
Confidence 4678888888888876 589999998873 2 2222110 00 001111111 2223444455554
Q ss_pred HHHHcCCccEEEEEEECCCCceeeEEEEeeeeccCCCCCCChhHHHHHHHHHHHHHHhhcc
Q 028781 71 LFIQKGLVERVAVIFSNANNVPLERYVFKIMVNQSYGSMVEEGHLEFSLRSFLIKLSVSKS 131 (204)
Q Consensus 71 ~~L~~g~l~kl~lvI~~~~~~~lEr~~Fdi~~~~~~~~~~~~~~ie~~~ra~L~~l~~~~~ 131 (204)
..-....|.++.+.+=..--.|-|-|..|+......+.+.+. ....=+|.++|.|..++.
T Consensus 130 ~lFs~t~Vp~VLILLGgt~~SPKE~YeInl~~l~~~s~e~sl-st~~clRkLfRsLf~aD~ 189 (264)
T PF06581_consen 130 QLFSLTLVPRVLILLGGTAVSPKEFYEINLERLVPNSKEQSL-STAVCLRKLFRSLFTADA 189 (264)
T ss_dssp HHHHHS---EEEEEESS-SSS-SEEEEEE-TTS--------S-HHHHHHHHHHHHHHHTTT
T ss_pred HHHhcCccceEEEEecCccCCcceeEEEcchhhccccccccc-ccHHHHHHHHHHHHcccc
Confidence 444566688876666444456889999998643222211122 345557777787777765
No 9
>KOG3874 consensus Uncharacterized conserved protein [Function unknown]
Probab=61.15 E-value=1e+02 Score=28.74 Aligned_cols=84 Identities=17% Similarity=0.269 Sum_probs=58.5
Q ss_pred ccceeeeccChhHHHHHHHHHHHHHHHHHcCCccEEEEEEECCCC--ceeeEEEEeeeeccCCCCCCChhHHHHHHHHHH
Q 028781 46 MNLVVQRARHPQLRDYIHSSVSSLLLFIQKGLVERVAVIFSNANN--VPLERYVFKIMVNQSYGSMVEEGHLEFSLRSFL 123 (204)
Q Consensus 46 ynl~v~~sr~p~l~~YI~~~l~~v~~~L~~g~l~kl~lvI~~~~~--~~lEr~~Fdi~~~~~~~~~~~~~~ie~~~ra~L 123 (204)
||+- +-.||++-.|...++.. .....|.-=+|.+.++..+| .++|-|..+.... .+.+.+...+++..+-..|
T Consensus 51 FN~a--I~d~pEV~~e~K~altg--~~p~vgl~lcvEisLkT~eGd~m~LE~W~L~~~at-eg~~~k~~~~~Ynrms~lL 125 (504)
T KOG3874|consen 51 FNMA--IDDLPEVSAELKSALTG--SYPPVGLTLCVEISLKTPEGDLMPLEAWILSSSAT-EGTDDKSRNELYNRMSTLL 125 (504)
T ss_pred hhhh--hhchHHHHHHHHHHhcc--CCCccCcceEEEEEEecCCCCeeeeehheeccccc-cCchhHHHHHHHHHHHHHH
Confidence 6666 47899999888888722 22233444477777888885 5899999988732 2233445668999999999
Q ss_pred HHHHhhcccCC
Q 028781 124 IKLSVSKSLSK 134 (204)
Q Consensus 124 ~~l~~~~~~Lp 134 (204)
+.|.++...-|
T Consensus 126 kSli~~tR~TP 136 (504)
T KOG3874|consen 126 KSLIVSTRMTP 136 (504)
T ss_pred HHHHHHhccCh
Confidence 99888766444
No 10
>TIGR02241 conserved hypothetical phage tail region protein. This family consists of uncharacterized proteins. All members so far represent bacterial genes found in apparent phage or otherwisely laterally transferred regions of the chromosome. Tentatively identified neighboring proteins tend to be phage tail region proteins. In some species, including Photorhabdus luminescens TTO1, several members of this family may be encoded near each other.
Probab=42.72 E-value=84 Score=24.35 Aligned_cols=46 Identities=13% Similarity=0.122 Sum_probs=34.6
Q ss_pred eeccChhHHHHHHHHHHHHHHHHHcCCccEEEEEEECCCCceeeEEEEee
Q 028781 51 QRARHPQLRDYIHSSVSSLLLFIQKGLVERVAVIFSNANNVPLERYVFKI 100 (204)
Q Consensus 51 ~~sr~p~l~~YI~~~l~~v~~~L~~g~l~kl~lvI~~~~~~~lEr~~Fdi 100 (204)
-+..++.|-+|+.+++.. -..+.-+.+.|.++|.++.++=||.|.=
T Consensus 62 G~~~~~~l~~W~~~~~~~----~~~~~rk~~~I~l~d~~g~~~~~W~~~~ 107 (140)
T TIGR02241 62 GVTNDSDLWQWANDSMLN----DMGTRRKNASIRLYNEAGEPLMRWEVIN 107 (140)
T ss_pred ccCCCHHHHHHHHHhhcc----cCcceeeEEEEEEECCCCCcEEEEEEEe
Confidence 345688899999988642 0023567888999999999999999953
No 11
>PF06327 DUF1053: Domain of Unknown Function (DUF1053); InterPro: IPR009398 Cyclic AMP (cAMP) is a ubiquitous signalling molecule which mediates many cellular processes by activating cAMP-dependent kinases and also inducing protein-protein interactions. This molecule is produced by the adenylate cyclase (AC) enzyme, using ATP as its substrate. Mammalian adenylate cyclase has nine closely related membrane-bound isoforms (AC1-9) showing significant sequence homology and sharing the same overall structure: two hydrophobic transmembrane domains, and two cytoplasmic domains that are responsible for the catalytic activity. These isoforms differ in both their tissue specificity and their regulation. Regulatory factors known to influence one or more of these isoforms include G proteins, protein kinases, calcium and calmodulin. For more information see [, ]. This entry represents a region of unknown function found in many of these isoforms. It is part of the N-terminal cytoplasmic domain but its presence is not necessary for catalytic activity []. ; GO: 0004016 adenylate cyclase activity, 0009190 cyclic nucleotide biosynthetic process, 0016021 integral to membrane
Probab=40.22 E-value=47 Score=24.06 Aligned_cols=38 Identities=8% Similarity=0.223 Sum_probs=31.5
Q ss_pred eccChhHHHHHHHHHHHHH-HHHHcCCccEEEEEEECCC
Q 028781 52 RARHPQLRDYIHSSVSSLL-LFIQKGLVERVAVIFSNAN 89 (204)
Q Consensus 52 ~sr~p~l~~YI~~~l~~v~-~~L~~g~l~kl~lvI~~~~ 89 (204)
.+-.++|++||..++++.. ..+.+.+++++.|.+.+++
T Consensus 50 ~~~eeevn~~l~~aIe~~S~~r~rse~~~~~tL~F~d~~ 88 (101)
T PF06327_consen 50 RSPEEEVNERLMQAIEARSSDRMRSEHINRFTLRFKDKS 88 (101)
T ss_pred cCcHHHHHHHHHHHHHHHHHHhHhhhhcceeeEEECChH
Confidence 3445789999999998876 5578999999999999875
No 12
>PF14242 DUF4342: Domain of unknown function (DUF4342)
Probab=38.87 E-value=39 Score=24.31 Aligned_cols=28 Identities=21% Similarity=0.279 Sum_probs=22.6
Q ss_pred hhHHHHHHHHHHHHHHHHHcCCccEEEE
Q 028781 56 PQLRDYIHSSVSSLLLFIQKGLVERVAV 83 (204)
Q Consensus 56 p~l~~YI~~~l~~v~~~L~~g~l~kl~l 83 (204)
..++..-+++++.+++.+.+|.++|+.+
T Consensus 9 e~~~~~g~~~~~~iK~li~kGNv~Ri~I 36 (84)
T PF14242_consen 9 EEFQVKGEELVDKIKELIKKGNVTRIII 36 (84)
T ss_pred ceeeecHHHHHHHHHHHHHhcCeEEEEE
Confidence 3344556789999999999999999865
No 13
>PF13103 TonB_2: TonB C terminal; PDB: 1LR0_A.
Probab=37.38 E-value=1.3e+02 Score=20.43 Aligned_cols=73 Identities=14% Similarity=0.059 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHH-----HcCCccEEEEEEECCCCceeeEEEEeeeeccCCCCCCChhHHHHHHHHHHHHHHhhcccCC
Q 028781 60 DYIHSSVSSLLLFI-----QKGLVERVAVIFSNANNVPLERYVFKIMVNQSYGSMVEEGHLEFSLRSFLIKLSVSKSLSK 134 (204)
Q Consensus 60 ~YI~~~l~~v~~~L-----~~g~l~kl~lvI~~~~~~~lEr~~Fdi~~~~~~~~~~~~~~ie~~~ra~L~~l~~~~~~Lp 134 (204)
.|...+...+.... ..+..+-.+-+-.+.+|.++ ...+. .+. -..++.++.+++|+ ..+.+|
T Consensus 3 ~Y~~~i~~~i~~~w~~p~~~~~~~~~~V~i~i~~dG~v~-~~~i~----~sS----G~~~~D~av~~ai~----~~~p~p 69 (85)
T PF13103_consen 3 SYFAQIQARIQQNWNPPPQDSGGLSVTVRITIDPDGRVI-SVRIV----KSS----GNPAFDAAVRRAIR----RASPFP 69 (85)
T ss_dssp -----HHHHHHHH----TT--TT--EEEEEEE-TTSBEE-EEEEE----E------S-HHHHHHHHHHHH----HH-B-G
T ss_pred chHHHHHHHHHHHcCCCCCCCCCcEEEEEEEECCCCCEE-EEEEe----cCC----CCHHHHHHHHHHHH----HcCCCC
Confidence 45555665555533 13344455555567778875 33332 111 13567777777777 334578
Q ss_pred CCC--CCeeEEEE
Q 028781 135 VLP--QGCRWEIT 145 (204)
Q Consensus 135 ~l~--~~~tF~i~ 145 (204)
+.| ..+..+|.
T Consensus 70 ~pP~~~~~~~~i~ 82 (85)
T PF13103_consen 70 PPPEYGKQPREIT 82 (85)
T ss_dssp GGG----------
T ss_pred cCCcccccccccc
Confidence 777 34444443
No 14
>PF09754 PAC2: PAC2 family; InterPro: IPR019151 This PAC2 (Proteasome assembly chaperone) family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 247 and 307 amino acids in length. These proteins function as a chaperone for the 26S proteasome, which is about 2000 kilodaltons (kDa) in molecular mass and contains one 20S core particle structure and two 19S regulatory caps. The 26S proteasome mediates ubiquitin-dependent proteolysis in eukaryotic cells. A number of studies including very recent ones have revealed that assembly of its 20S catalytic core particle is an ordered process that involves several conserved proteasome assembly chaperones (PACs). Two heterodimeric chaperones, PAC1-PAC2 and PAC3-PAC4, promote the assembly of rings composed of seven alpha subunits [, , , ].; PDB: 3MNF_A 2P90_B 3E35_A 3GAA_D 2WAM_C.
Probab=37.07 E-value=26 Score=28.65 Aligned_cols=50 Identities=20% Similarity=0.135 Sum_probs=36.4
Q ss_pred CCCcccceeeeccceeeeccChhHHHHHHHHHHHHHHHHHcCCccEEEEE
Q 028781 35 YPSGAFERRRYMNLVVQRARHPQLRDYIHSSVSSLLLFIQKGLVERVAVI 84 (204)
Q Consensus 35 YP~~~F~~~r~ynl~v~~sr~p~l~~YI~~~l~~v~~~L~~g~l~kl~lv 84 (204)
.|+--|-..+.-++-+.++|-|....+..++.+.+.+|+.+..++++++.
T Consensus 56 ~~~~~iy~~~~~~i~vl~~~~p~~~~~~~~f~~~l~~~~~~~g~~~vi~l 105 (219)
T PF09754_consen 56 SPPLEIYYSEDSKILVLQGRSPIPPGRWYEFAEELLDWIKSFGVKEVIVL 105 (219)
T ss_dssp B-SEEEEEEECTTEEEEEESSE--SCGHHHHHHHHHHHHHHTTECEEEEE
T ss_pred ccceEEEEECCCCEEEEEecCCCCchHHHHHHHHHHHHHHHcCCCEEEEE
Confidence 33333333444457888899999999999999999999999999988753
No 15
>PF06841 Phage_T4_gp19: T4-like virus tail tube protein gp19; InterPro: IPR010667 This family consists of several tail tube protein gp19 sequences from the T4-like viruses [,]. The contractile tail of bacteriophage T4 consists of a contractile sheath, a tube and a baseplate. Protomers of Gp19 form the tail tube, which penetrates the outer membrane of Escherichia coli upon infection.; GO: 0005198 structural molecule activity
Probab=34.04 E-value=1.5e+02 Score=22.09 Aligned_cols=46 Identities=11% Similarity=0.260 Sum_probs=33.6
Q ss_pred eeccChhHHHHHHHHHHHHHHHHHcCCccEEEEEEECCCCceeeEEEEee
Q 028781 51 QRARHPQLRDYIHSSVSSLLLFIQKGLVERVAVIFSNANNVPLERYVFKI 100 (204)
Q Consensus 51 ~~sr~p~l~~YI~~~l~~v~~~L~~g~l~kl~lvI~~~~~~~lEr~~Fdi 100 (204)
.++....|-+|+..+...-. .+.-+.+.|.++|.++.++=||.|.=
T Consensus 58 g~~~~~~l~~W~~~~~~~~~----~~~~~~~~I~lld~~~~~~~~w~~~~ 103 (134)
T PF06841_consen 58 GVDESSDLWDWFNAINNGES----NSARKDISIELLDSDGKPVARWNFRN 103 (134)
T ss_pred eccCcHHHHHHHHHHhcccc----ccccceEEEEEECCCCCEEEEEEEEe
Confidence 55668888888887664321 22378899999999987777999953
No 16
>cd02969 PRX_like1 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic cysteine found in PRXs, which aligns to the second cysteine in the CXXC motif of TRX. In addition, these proteins do not contain the other two conserved residues of the catalytic triad of PRX. PRXs confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF.
Probab=29.04 E-value=80 Score=24.60 Aligned_cols=58 Identities=10% Similarity=0.006 Sum_probs=32.4
Q ss_pred EEEEECCCCceeeEEEEeeeeccCCCCCCChhHHHHHHHHHHHHHHhhcccCCCCCCCe
Q 028781 82 AVIFSNANNVPLERYVFKIMVNQSYGSMVEEGHLEFSLRSFLIKLSVSKSLSKVLPQGC 140 (204)
Q Consensus 82 ~lvI~~~~~~~lEr~~Fdi~~~~~~~~~~~~~~ie~~~ra~L~~l~~~~~~Lp~l~~~~ 140 (204)
...|+|++|+++-++.++-... ......+..++..++++.|..=.......|...+.|
T Consensus 112 ~~~lid~~G~v~~~~~~~~~~~-~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~ 169 (171)
T cd02969 112 DFFLFDPDGKLVYRGRIDDSRP-GNDPPVTGRDLRAALDALLAGKPVPVPQTPSIGCSI 169 (171)
T ss_pred cEEEECCCCeEEEeecccCCcc-cccccccHHHHHHHHHHHHcCCCCCccccCCCCccc
Confidence 4788898888876666542111 101234567788888777665444444444333333
No 17
>PF09652 Cas_VVA1548: Putative CRISPR-associated protein (Cas_VVA1548); InterPro: IPR013443 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved region of about 95 amino acids found exclusively in species with CRISPR repeats. In all bacterial species that contain this entry, the genes encoding the proteins are in the midst of a cluster of cas genes.
Probab=27.72 E-value=36 Score=25.08 Aligned_cols=14 Identities=21% Similarity=0.396 Sum_probs=12.0
Q ss_pred eeccChhHHHHHHH
Q 028781 51 QRARHPQLRDYIHS 64 (204)
Q Consensus 51 ~~sr~p~l~~YI~~ 64 (204)
++||||+..+|+..
T Consensus 2 fIsRH~GAieW~~~ 15 (93)
T PF09652_consen 2 FISRHPGAIEWAKQ 15 (93)
T ss_pred eeeecccHHHHHHH
Confidence 48999999999865
No 18
>PF10259 Rogdi_lz: Rogdi leucine zipper containing protein
Probab=26.18 E-value=4.2e+02 Score=22.94 Aligned_cols=85 Identities=15% Similarity=0.150 Sum_probs=48.8
Q ss_pred hHHHHHHHHHHHHHHHHHcCCccEEEEEEECCCCceeeEEEEeeeeccCCCCCCChhHHHHHHHHHHHHHHhhc------
Q 028781 57 QLRDYIHSSVSSLLLFIQKGLVERVAVIFSNANNVPLERYVFKIMVNQSYGSMVEEGHLEFSLRSFLIKLSVSK------ 130 (204)
Q Consensus 57 ~l~~YI~~~l~~v~~~L~~g~l~kl~lvI~~~~~~~lEr~~Fdi~~~~~~~~~~~~~~ie~~~ra~L~~l~~~~------ 130 (204)
.+..||+.++..+......++... ...+..++-..++.++..|...-
T Consensus 91 ~~~n~l~~al~~L~~~~~~~~~~~---------------------------~~~~~~~l~~~L~~l~~~L~~ar~~L~~P 143 (273)
T PF10259_consen 91 DARNHLNQALDLLDDLQSIYDPEE---------------------------FFKDANELLSQLRNLMNSLQEARNSLKLP 143 (273)
T ss_pred HHHHHHHHHHHHHHhhhhcccccc---------------------------ccccHHHHHHHHHHHHHHHHHHHHhhcCC
Confidence 456777777776655554443322 11345667777777777665431
Q ss_pred ---------------ccCCCCCCCeeEEEEEEEeeCCC--CCCC-CCCCCceecCc
Q 028781 131 ---------------SLSKVLPQGCRWEITAYFCSLPQ--VNTS-KDAELWIPTDT 168 (204)
Q Consensus 131 ---------------~~Lp~l~~~~tF~i~v~~~~~~~--~~~~-~~~~~Wi~~d~ 168 (204)
.|-|+||.+++|++.+.-.+..- .... ..+.+|-..|+
T Consensus 144 ~~~~~~~~~~~~~~~~F~P~Lp~~ls~~~~I~~~~Lvl~~~~L~~~~~~p~~~i~~ 199 (273)
T PF10259_consen 144 SDPNLWEPQSSPPSHSFCPPLPPDLSFDFYIQDNELVLDLRQLEPVTPKPWCEIDS 199 (273)
T ss_pred CCCCccccccCCcccccCCCCCcceEEEEEEecceeeeeeeeeEEccccccccccC
Confidence 27899999999987653322110 0111 13578988884
No 19
>PF02603 Hpr_kinase_N: HPr Serine kinase N terminus; InterPro: IPR011126 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents the N-terminal region of Hpr Serine/threonine kinase PtsK. This kinase is the sensor in a multicomponent phosphorelay system in control of carbon catabolic repression in bacteria []. This kinase in unusual in that it recognises the tertiary structure of its target and is a member of a novel family unrelated to any previously described protein phosphorylating enzymes []. X-ray analysis of the full-length crystalline enzyme from Staphylococcus xylosus at a resolution of 1.95 A shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller. The blades are formed by two N-terminal domains each, and the compact central hub assembles the C-terminal kinase domains []. ; GO: 0000155 two-component sensor activity, 0004672 protein kinase activity, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0006109 regulation of carbohydrate metabolic process; PDB: 1KNX_B 1KO7_A.
Probab=26.16 E-value=13 Score=28.49 Aligned_cols=51 Identities=14% Similarity=0.187 Sum_probs=34.0
Q ss_pred CCChHHHHHHHHHHHHHHHHHhhhccCCCCCcccc-eeeeccceeeeccChh
Q 028781 7 QSPQVETARILAEFLEVAITSVVFLKGLYPSGAFE-RRRYMNLVVQRARHPQ 57 (204)
Q Consensus 7 ~~~~~~s~~~v~efLevaih~ILY~R~vYP~~~F~-~~r~ynl~v~~sr~p~ 57 (204)
+++.++-...+.+++..-+=+|..-||.=|++.|. ..++||+|+..|..+.
T Consensus 64 ~l~~~~r~~~l~~l~~~~~P~iIvt~~~~~p~~l~e~a~~~~ipll~t~~~t 115 (127)
T PF02603_consen 64 SLDEEERKERLEKLFSYNPPCIIVTRGLEPPPELIELAEKYNIPLLRTPLST 115 (127)
T ss_dssp CS-HHHHCCHHHHHCTTT-S-EEEETTT---HHHHHHHHHCT--EEEESS-H
T ss_pred HCCHHHHHHHHHHHhCCCCCEEEEECcCCCCHHHHHHHHHhCCcEEEcCCcH
Confidence 45566667788999999999999999998777654 5567999999998875
No 20
>PF09457 RBD-FIP: FIP domain ; InterPro: IPR019018 The Rab11 GTPase regulates recycling of internalized plasma membrane receptors and is essential for completion of cytokinesis. A family of Rab11 interacting proteins (FIPs) that conserve a C-terminal Rab-binding domain (RBD) selectively recognise the active form of Rab11. FIPs are diverse in sequence length and composition toward their N-termini, presumably a feature that underpins their specific roles in Rab11-mediated vesicle trafficking. They have been divided into three subfamilies (classe I, II, and III)on the basis of domain architecture. Class I FIPs comprises a subfamily of three proteins (Rip11/pp75/FIP5, Rab-coupling protein (RCP), and FIP2) that possess an N- terminal C2 domain, localize to recycling endosomes, and regulate plasma membrane recycling. The class II subfamily consists of two proteins (FIP3/eferin/arfophilin and FIP4) with tandem EF hands and a proline-rich region. Class II FIPs localize to recycling endosomes, the trans-Golgi network, and have been implicated in the regulation of membrane trafficking during cytokinesis. The class III subfamily consists of a single protein, FIP1, which does not contain obvious homology domains or motifs other than the FIP-RBD [, , , ]. The FIP-RBD domain is also found in Rab6-interacting protein Erc1/Elks. Erc1 is the regulatory subunit of the IKK complex and probably recruits IkappaBalpha/NFKBIA to the complex []. It may be involved in the organisation of the cytomatrix at the nerve terminals active zone (CAZ) which regulates neurotransmitter release. It may also be involved in vesicle trafficking at the CAZ, as well as in Rab-6 regulated endosomes to Golgi transport []. The FIB-RBD domain consists of an N-terminal long alpha-helix, followed by a 90 degrees bend at a conserved proline residue, a 3(10) helix and a C-terminal short beta-strand, adopting an "L" shape. The long alpha-helix forms a parallel coiled-coil homodimer that symmetrically interacts with two Rab11 molecules on both sides, forming a quaternary Rab11-(FIP)2-Rab11 complex. The Rab11-interacting region of FIP-RBD is confined to the C-terminal 24 amino acids, which cover the C-terminal half of the long alpha-helix and the short beta-strand [, , , ]. This entry represents the FIP-RBD domain.; PDB: 2HV8_E 2D7C_D 2K6S_B 2GZD_D 2GZH_B.
Probab=24.33 E-value=40 Score=21.77 Aligned_cols=18 Identities=28% Similarity=0.554 Sum_probs=14.0
Q ss_pred ccChhHHHHHHHHHHHHH
Q 028781 53 ARHPQLRDYIHSSVSSLL 70 (204)
Q Consensus 53 sr~p~l~~YI~~~l~~v~ 70 (204)
++.-+|.+||++++..|.
T Consensus 21 ~~v~eLe~YiD~LL~rVm 38 (48)
T PF09457_consen 21 SRVRELEDYIDNLLVRVM 38 (48)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 345579999999998765
No 21
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=23.82 E-value=1.6e+02 Score=19.25 Aligned_cols=33 Identities=6% Similarity=0.055 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHcCCccEEEEEEECCCCceeeEEEE
Q 028781 64 SSVSSLLLFIQKGLVERVAVIFSNANNVPLERYVF 98 (204)
Q Consensus 64 ~~l~~v~~~L~~g~l~kl~lvI~~~~~~~lEr~~F 98 (204)
+++...+....+ -....|+|++.+|.+-|++.|
T Consensus 30 eAi~~Ar~~a~~--~~~~el~Ih~~dG~i~~~~sy 62 (62)
T PF09954_consen 30 EAIEAARELAKN--QGGGELIIHGRDGKIREERSY 62 (62)
T ss_pred HHHHHHHHHHHh--CCCcEEEEECCCCeEEEeecC
Confidence 566666666644 126789999999998888754
No 22
>KOG3744 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.77 E-value=80 Score=27.55 Aligned_cols=30 Identities=17% Similarity=0.201 Sum_probs=26.7
Q ss_pred CCcccCCCChHHHHHHHHHHHHHHHHHhhh
Q 028781 1 MDRSDAQSPQVETARILAEFLEVAITSVVF 30 (204)
Q Consensus 1 ~~~~~~~~~~~~s~~~v~efLevaih~ILY 30 (204)
||+|+-..++.+....++-|+|++|..|+=
T Consensus 77 ~~~k~~rts~~~l~~~~~a~~E~~iaaiia 106 (311)
T KOG3744|consen 77 WYSKKKRTSSSALFETLCAILENAIAAIIA 106 (311)
T ss_pred HHhccccccHHHHHHHHHHHHHHHHHHHHH
Confidence 578887889999999999999999999864
No 23
>PRK05428 HPr kinase/phosphorylase; Provisional
Probab=22.18 E-value=98 Score=27.63 Aligned_cols=80 Identities=16% Similarity=0.174 Sum_probs=56.4
Q ss_pred CCChHHHHHHHHHHHHHHHHHhhhccCCCCCcc-cceeeeccceeeeccChhHHHHHHHHHHHHHHHHH-cCCccEEEEE
Q 028781 7 QSPQVETARILAEFLEVAITSVVFLKGLYPSGA-FERRRYMNLVVQRARHPQLRDYIHSSVSSLLLFIQ-KGLVERVAVI 84 (204)
Q Consensus 7 ~~~~~~s~~~v~efLevaih~ILY~R~vYP~~~-F~~~r~ynl~v~~sr~p~l~~YI~~~l~~v~~~L~-~g~l~kl~lv 84 (204)
+++.++-...+..++..-+-+|...||.-|++. .+..+++|+|++.|..+. ...|+.+..-+...+. +-.++-..+.
T Consensus 65 ~l~~~~r~~~~~~l~~~~~P~iIvt~~~~~p~~l~~~a~~~~ipll~t~~~t-~~~i~~l~~~L~~~la~~~~iHg~~v~ 143 (308)
T PRK05428 65 QLSEEERKERLKKLFSLEPPCIIVTRGLEPPPELLEAAKEAGIPLLRTPLST-TRLISKLTNYLDRKLAPRTSVHGVLVD 143 (308)
T ss_pred hCCHHHHHHHHHHHhCCCCCEEEEECcCCCCHHHHHHHHHcCCcEEEeCCcH-HHHHHHHHHHHHHHhhhcceeeeEEEE
Confidence 467788888999999999999999999999986 455567999999999865 4444444444444442 2345554444
Q ss_pred EEC
Q 028781 85 FSN 87 (204)
Q Consensus 85 I~~ 87 (204)
|+.
T Consensus 144 V~G 146 (308)
T PRK05428 144 IYG 146 (308)
T ss_pred ECC
Confidence 443
No 24
>PRK14133 DNA polymerase IV; Provisional
Probab=20.75 E-value=5.8e+02 Score=22.41 Aligned_cols=83 Identities=7% Similarity=0.044 Sum_probs=53.5
Q ss_pred CCcccceeeeccceeeeccChhHHHHHHHHHHHHHHHHHcCC--ccEEEEEEECCCCceeeEEEEeeeeccCCCCCCChh
Q 028781 36 PSGAFERRRYMNLVVQRARHPQLRDYIHSSVSSLLLFIQKGL--VERVAVIFSNANNVPLERYVFKIMVNQSYGSMVEEG 113 (204)
Q Consensus 36 P~~~F~~~r~ynl~v~~sr~p~l~~YI~~~l~~v~~~L~~g~--l~kl~lvI~~~~~~~lEr~~Fdi~~~~~~~~~~~~~ 113 (204)
|+.+|...+-|+-+ +....++..++..++..+...|.+.. .+++.|.+...+....-+ ...+... ..+..
T Consensus 236 ~~ksi~~~~~~~~~--~~~~~~l~~~l~~L~~~l~~rL~~~~~~~~~l~l~l~~~~~~~~~~-~~~l~~~-----t~~~~ 307 (347)
T PRK14133 236 ERKSIGKETTLKKD--TKDKEELKKYLKDFSNIISEELKKRNLYGKTVTVKIKTSDFQTHTK-SKTLNDY-----IRDKE 307 (347)
T ss_pred CCcceEeeEEcCCC--CCCHHHHHHHHHHHHHHHHHHHHhcCCCcceEEEEEEECCCCeeEE-EEECCCC-----cCCHH
Confidence 34455555555554 45668899999999999999997664 667888887654333222 2222211 12456
Q ss_pred HHHHHHHHHHHHH
Q 028781 114 HLEFSLRSFLIKL 126 (204)
Q Consensus 114 ~ie~~~ra~L~~l 126 (204)
++...++..|.++
T Consensus 308 ~l~~l~~~lle~~ 320 (347)
T PRK14133 308 EIYNVACEILEHI 320 (347)
T ss_pred HHHHHHHHHHHhc
Confidence 7888888887776
Done!