Query 028572
Match_columns 207
No_of_seqs 130 out of 352
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 13:37:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028572.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028572hhsearch_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 9.8E-74 2.1E-78 465.8 16.0 201 3-203 2-203 (203)
2 KOG3186 Mitotic spindle checkp 100.0 7.7E-44 1.7E-48 289.3 14.6 182 15-200 5-198 (202)
3 PF02301 HORMA: HORMA domain; 100.0 4E-33 8.7E-38 233.4 17.6 177 12-191 1-208 (208)
4 KOG4652 HORMA domain [Chromati 99.4 4.5E-12 9.7E-17 112.3 11.4 186 12-197 8-217 (324)
5 PF07855 DUF1649: Protein of u 98.5 2.7E-06 5.9E-11 69.8 11.6 127 17-146 7-158 (163)
6 PF10033 ATG13: Autophagy-rela 95.1 1.1 2.4E-05 38.5 14.1 170 20-202 1-230 (233)
7 KOG4493 Uncharacterized conser 91.6 1.5 3.2E-05 37.5 8.6 140 19-159 16-183 (219)
8 PF06581 p31comet: Mad1 and Cd 80.2 33 0.00071 30.4 10.9 145 9-168 53-216 (264)
9 PF02603 Hpr_kinase_N: HPr Ser 52.6 4.6 9.9E-05 31.4 -0.0 49 12-60 66-115 (127)
10 PF04386 SspB: Stringent starv 52.6 33 0.00072 27.7 5.0 52 125-177 8-60 (155)
11 PF10259 Rogdi_lz: Rogdi leuci 51.1 1.2E+02 0.0026 26.7 8.7 34 140-173 159-200 (273)
12 COG0768 FtsI Cell division pro 49.8 33 0.00071 33.5 5.4 47 47-97 235-281 (599)
13 KOG3874 Uncharacterized conser 44.9 2.8E+02 0.0061 26.4 10.4 132 55-201 55-192 (504)
14 PRK05428 HPr kinase/phosphoryl 37.2 62 0.0013 29.3 4.7 78 11-89 66-145 (308)
15 PF14242 DUF4342: Domain of un 35.2 46 0.001 24.3 3.0 28 59-86 9-36 (84)
16 PF09754 PAC2: PAC2 family; I 33.2 16 0.00035 30.3 0.4 51 37-87 55-105 (219)
17 PF09457 RBD-FIP: FIP domain ; 33.1 23 0.00049 23.4 0.9 18 56-73 21-38 (48)
18 PF06327 DUF1053: Domain of Un 32.9 68 0.0015 23.5 3.7 38 55-92 50-88 (101)
19 cd00552 RaiA RaiA ("ribosome-a 27.4 2.1E+02 0.0045 20.1 5.4 36 55-92 9-44 (93)
20 PF07607 DUF1570: Protein of u 24.4 37 0.00081 26.7 1.0 16 27-42 9-24 (128)
21 PRK15105 peptidoglycan synthas 23.4 1.8E+02 0.0039 28.4 5.6 47 48-97 226-272 (578)
22 COG3814 Uncharacterized protei 22.6 2.2E+02 0.0047 23.2 5.0 37 123-160 11-47 (157)
23 PF06841 Phage_T4_gp19: T4-lik 21.6 2.1E+02 0.0045 21.6 4.7 46 55-105 59-104 (134)
24 TIGR02071 PBP_1b penicillin-bi 21.4 1.9E+02 0.0042 29.2 5.5 50 48-97 367-419 (730)
25 TIGR02074 PBP_1a_fam penicilli 20.9 1.7E+02 0.0037 28.2 4.9 50 48-97 219-270 (530)
26 TIGR02073 PBP_1c penicillin-bi 20.7 2E+02 0.0042 29.0 5.4 46 52-97 243-288 (727)
27 cd08641 DNA_pol_gammaA Pol gam 20.1 3.9E+02 0.0085 25.4 6.9 89 46-156 316-406 (425)
No 1
>KOG3285 consensus Spindle assembly checkpoint protein [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=100.00 E-value=9.8e-74 Score=465.77 Aligned_cols=201 Identities=58% Similarity=0.945 Sum_probs=192.4
Q ss_pred cccccccceehhhHHHHHHHHHHHhhhhhhhccCCCCCCcchhhhhcCCccccccCHhHHHHHHHHHHHHHHHHHcCccc
Q 028572 3 SRTVAKDIITLRGSAAIVSEFFGYAANSILYNRGVYPEESFVKVKKYGLPMLLTEDEGVKSFIANLTAQLSEWLEAGKLQ 82 (207)
Q Consensus 3 ~~~~~~~~itl~~s~~~v~efLe~aih~ILy~RgiYP~~~F~~~r~y~l~v~~sr~p~l~~YI~~~l~~v~~~L~~g~v~ 82 (207)
++.++++.||||||+++|+|||+|+||+|||||||||+|+|.++||||++++++.+++|+.||++++.|+++||.+|+++
T Consensus 2 ~~~~~~~~isLkGSa~iV~EFf~y~iNSILyQRgiYPaEdF~~vkKYgLtllvs~D~elk~f~~~ilsQ~~~WL~~~kiq 81 (203)
T KOG3285|consen 2 TAVATKNCISLKGSAQIVSEFFEYGINSILYQRGIYPAEDFVRVKKYGLTLLVSHDEELKTFIRNILSQVHEWLSKGKIQ 81 (203)
T ss_pred ccccccceeEeechHHHHHHHHHhhhhHHHHhccCCcHHHhhHHHhcCceEEEecCHHHHHHHHHHHHHHHHHHHhCCcc
Confidence 44678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEEEEeCCCcceeEEEeeeccccccccccc-cCCcCCHHHHHHHHHHHHHHHHhhhhcCCCCCCCceEEEEEEecCCC
Q 028572 83 RVVLVIMSKATKEVLERWNFSIETDNEVVEKG-VSREKSDKEIMREIQAIMRQIASSITYLPCLDETCVFDVLAYTDKDV 161 (207)
Q Consensus 83 kl~lvI~~~~~~e~lEr~~Fdi~~~~~~~~~~-~~~~~~~~~i~~eiRa~l~qI~~s~~~Lp~L~~~ctF~vlv~t~~~~ 161 (207)
||+|||.++.++|++|||.||++....+.+.+ ....++++.+|+||||+||||+++++|||.|++.|||+|++||+.|.
T Consensus 82 klvlvI~~~~tgEvlErWqFnie~~~~~~d~~na~~~k~~~~iq~EIraviRQItasVtfLP~Le~~ctFdvLiyTdkD~ 161 (203)
T KOG3285|consen 82 KLVLVITSKHTGEVLERWQFNIETENTASDGQNATRVKDLKRIQNEIRAVIRQITASVTFLPLLEEICTFDVLIYTDKDT 161 (203)
T ss_pred eEEEEEEecccccchhheeeeeeeeccccCcccccchhHHHHHHHHHHHHHHHHhhheeecccccceeEEEEEEEeCCCc
Confidence 99999999999999999999999988776554 45668899999999999999999999999999999999999999999
Q ss_pred CCCCccccCCcccccCCceeeeeeeecCceeeeeEEEEecCc
Q 028572 162 AVPFTWIESDPKLIANPQMVKLHSFDTKIHKVDTLVSYKNDE 203 (207)
Q Consensus 162 ~~p~~Wi~sd~~~i~n~~~v~lrsfsT~~h~v~~~V~y~~~~ 203 (207)
.+|..|++|+|+.|+||+.|+||||||++|||++.|+||.+.
T Consensus 162 ~vP~~W~eS~~~~I~n~e~VqlrsFsT~~HKVdt~V~YK~~~ 203 (203)
T KOG3285|consen 162 EVPEKWDESGPKLIQNPEAVQLRSFSTSIHKVDTQVSYKMDT 203 (203)
T ss_pred cCCcchhcCCCeEecChhhEEEeeccccceeecceEEeccCC
Confidence 999999999999999999999999999999999999999863
No 2
>KOG3186 consensus Mitotic spindle checkpoint protein [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=7.7e-44 Score=289.35 Aligned_cols=182 Identities=23% Similarity=0.356 Sum_probs=161.6
Q ss_pred hHHHHHHHHHHHhhhhhhhccCCCCCCcchhhhhcCCccccccCHhHHHHHHHHHHHHHHHHHcCccceEEEEEEeCCCc
Q 028572 15 GSAAIVSEFFGYAANSILYNRGVYPEESFVKVKKYGLPMLLTEDEGVKSFIANLTAQLSEWLEAGKLQRVVLVIMSKATK 94 (207)
Q Consensus 15 ~s~~~v~efLe~aih~ILy~RgiYP~~~F~~~r~y~l~v~~sr~p~l~~YI~~~l~~v~~~L~~g~v~kl~lvI~~~~~~ 94 (207)
..++.++||+|+++|+|||.|++||.++|.++|+||.|||+||||.||+||.++|++++++|++|.|++++|+|+++++.
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 45789999999999999999999999999999999999999999999999999999999999999999999999999975
Q ss_pred ceeEEEeeeccccccccccccCCcCCHHHHHHHHHHHHHHHHhhhhcCCCCCCC-ceEEEEEEecCCCC---------CC
Q 028572 95 EVLERWNFSIETDNEVVEKGVSREKSDKEIMREIQAIMRQIASSITYLPCLDET-CVFDVLAYTDKDVA---------VP 164 (207)
Q Consensus 95 e~lEr~~Fdi~~~~~~~~~~~~~~~~~~~i~~eiRa~l~qI~~s~~~Lp~L~~~-ctF~vlv~t~~~~~---------~p 164 (207)
.+|||+|.++..+...+... .-+.++++.+||+|.||+.+..-||.+|++ |||+|++||++.+. .|
T Consensus 85 -~~E~yvf~~~s~p~~~~~~d---~~l~~~eq~mRa~i~kis~~~n~lp~~p~G~Ctftv~vht~~~a~r~~~~~~~~~~ 160 (202)
T KOG3186|consen 85 -EEERYVFSTDSIPIIPDFLD---EFLDAYEQYMRASIIKISNITNGLPLIPQGICTFTVRVHTKDGAPRPKQWEEWFLP 160 (202)
T ss_pred -hhhheEeeccCCCcCchhHH---HHHHHHHHHHHHHHHHHHHhhcCCCCCCCceeEEEEEEEeccccccCcchHHhhcC
Confidence 89999999998776433211 135678999999999999999999999988 99999999998754 35
Q ss_pred CccccCCcc--cccCCceeeeeeeecCceeeeeEEEEe
Q 028572 165 FTWIESDPK--LIANPQMVKLHSFDTKIHKVDTLVSYK 200 (207)
Q Consensus 165 ~~Wi~sd~~--~i~n~~~v~lrsfsT~~h~v~~~V~y~ 200 (207)
+||+-++.. ...+.-.+|||.++.+++||+.+|+-+
T Consensus 161 FPw~~~~~~~~q~~gv~liPl~~vd~~~lkm~i~ve~~ 198 (202)
T KOG3186|consen 161 FPWARETDATRQFKGVILIPLRNVDIGPLKMEIWVEKY 198 (202)
T ss_pred CchhhcchhhhhccCcEEEeeeecccCceEEEEEEEee
Confidence 688866644 456678999999999999999999754
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=4e-33 Score=233.43 Aligned_cols=177 Identities=31% Similarity=0.446 Sum_probs=138.9
Q ss_pred ehhhHHHHHHHHHHHhhhhhhhccCCCCCCcchhhhhcCCcc------ccccCHhHHHHHHHHHHHHHHHHHcCccceEE
Q 028572 12 TLRGSAAIVSEFFGYAANSILYNRGVYPEESFVKVKKYGLPM------LLTEDEGVKSFIANLTAQLSEWLEAGKLQRVV 85 (207)
Q Consensus 12 tl~~s~~~v~efLe~aih~ILy~RgiYP~~~F~~~r~y~l~v------~~sr~p~l~~YI~~~l~~v~~~L~~g~v~kl~ 85 (207)
|.++|+.++++||++|||+|||+||+||++.|++++.||+.+ +.++||.|++||++ ++.++|.+|.|++|+
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 678999999999999999999999999999999999998888 79999999999988 999999999999999
Q ss_pred EEEEeC---CCcceeEEEeeecccccccccccc-------------CCcCCHHHHHHHHHHHHHHHHhhhhcCCCCCCC-
Q 028572 86 LVIMSK---ATKEVLERWNFSIETDNEVVEKGV-------------SREKSDKEIMREIQAIMRQIASSITYLPCLDET- 148 (207)
Q Consensus 86 lvI~~~---~~~e~lEr~~Fdi~~~~~~~~~~~-------------~~~~~~~~i~~eiRa~l~qI~~s~~~Lp~L~~~- 148 (207)
++|++. ++++++|||+|++++.+...+... ....+..++++++|++|++|..+.+.||+||++
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 456899999999999765432110 013578899999999999999999999999876
Q ss_pred -ceEEEEEEec--CCCCCCC-ccccC--Ccc--cccCCceeeeeeeecCce
Q 028572 149 -CVFDVLAYTD--KDVAVPF-TWIES--DPK--LIANPQMVKLHSFDTKIH 191 (207)
Q Consensus 149 -ctF~vlv~t~--~~~~~p~-~Wi~s--d~~--~i~n~~~v~lrsfsT~~h 191 (207)
++|+|.++.+ ++...|. .|.+. ... .-.+++.|++++++|+.|
T Consensus 158 ~~~~~l~~~~~tp~dy~pp~f~~~~~~~~~~~~~~~~~~~~~vg~v~t~~H 208 (208)
T PF02301_consen 158 TLTFKLLYYDDTPEDYEPPGFEAAEEATSFPLIFDEEPERVSVGSVSTGHH 208 (208)
T ss_dssp SEEEEEEEEES-ETTSCSST-TEEES--STEEESSCSEEEEEEEEEEESSE
T ss_pred eEEEEEEEEeCCCccccCCCCCCcccccccccccccceEEEEEeeeeCCCC
Confidence 6667777763 2333332 45544 222 224568999999999998
No 4
>KOG4652 consensus HORMA domain [Chromatin structure and dynamics]
Probab=99.37 E-value=4.5e-12 Score=112.34 Aligned_cols=186 Identities=22% Similarity=0.305 Sum_probs=138.5
Q ss_pred ehhhHHHHHHHHHHHhhhhhhhccCCCCCCcchhhhhcC--Ccccc-ccCHhHHH-HHHHHHHHHHHHHHcCccceEEEE
Q 028572 12 TLRGSAAIVSEFFGYAANSILYNRGVYPEESFVKVKKYG--LPMLL-TEDEGVKS-FIANLTAQLSEWLEAGKLQRVVLV 87 (207)
Q Consensus 12 tl~~s~~~v~efLe~aih~ILy~RgiYP~~~F~~~r~y~--l~v~~-sr~p~l~~-YI~~~l~~v~~~L~~g~v~kl~lv 87 (207)
.-++|..++++.|.+|+-.|||.|||.|.+.|..+.-++ +-+-. .+.|.=.. -|..++..+...+..|.++++.++
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 446899999999999999999999999999999988887 43332 22222221 266667788888899999999999
Q ss_pred EEeCCCcceeEEEeeecccccccccc-----ccC-Cc--------CCHHHHHHHHHHHHHHHHhhhhcCCCCCCCceEEE
Q 028572 88 IMSKATKEVLERWNFSIETDNEVVEK-----GVS-RE--------KSDKEIMREIQAIMRQIASSITYLPCLDETCVFDV 153 (207)
Q Consensus 88 I~~~~~~e~lEr~~Fdi~~~~~~~~~-----~~~-~~--------~~~~~i~~eiRa~l~qI~~s~~~Lp~L~~~ctF~v 153 (207)
|++.++.+.+|.|+|.+.++....-. +.. ++ .+..+..+++...+||+--+...|-+||++|.-.-
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 99999889999999999997654211 000 00 12234678899999999999999999998776654
Q ss_pred EEEecCC---CCCCCccccCCccc---ccCCceeeeeeeecCceeeeeEE
Q 028572 154 LAYTDKD---VAVPFTWIESDPKL---IANPQMVKLHSFDTKIHKVDTLV 197 (207)
Q Consensus 154 lv~t~~~---~~~p~~Wi~sd~~~---i~n~~~v~lrsfsT~~h~v~~~V 197 (207)
.+|=++. ...|...-++++.. =.|++.+-+...+|++|++...|
T Consensus 168 rl~Y~e~~ppDyqP~gFkd~~~~~y~~p~~p~~~~IG~v~~~hH~~~~kv 217 (324)
T KOG4652|consen 168 RLYYTERVPPDYQPEGFKDSTRAFYTLPVNPEQINIGAVSTPHHKGFVKV 217 (324)
T ss_pred eeeecccCCccCCCcccccCccceeecCCCccceeeccccCccceeEEEE
Confidence 4444332 23466677775332 24788899999999999887755
No 5
>PF07855 DUF1649: Protein of unknown function (DUF1649); InterPro: IPR012445 This family represents Autophagy-related protein 101.
Probab=98.47 E-value=2.7e-06 Score=69.75 Aligned_cols=127 Identities=17% Similarity=0.235 Sum_probs=94.4
Q ss_pred HHHHHHHHHHhhhhhhhccCCCCCCcch--hhhhcCCccccccCHhHHHHHHHHHHHHHHHHHcCccc--------eEEE
Q 028572 17 AAIVSEFFGYAANSILYNRGVYPEESFV--KVKKYGLPMLLTEDEGVKSFIANLTAQLSEWLEAGKLQ--------RVVL 86 (207)
Q Consensus 17 ~~~v~efLe~aih~ILy~RgiYP~~~F~--~~r~y~l~v~~sr~p~l~~YI~~~l~~v~~~L~~g~v~--------kl~l 86 (207)
...+.|-+...+|+|||+|-+ ++=.-. .+-.+|++.-.+.+|+|..-|++-+.++.+||.++.-. .|.|
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 345899999999999999943 222223 45677999889999999999999999999999887654 7888
Q ss_pred EEEeCCCc-----------ceeEEEeeeccccccccccccCCcCCHHHHHHHHHHHHHHHHhhh----hcCCCCC
Q 028572 87 VIMSKATK-----------EVLERWNFSIETDNEVVEKGVSREKSDKEIMREIQAIMRQIASSI----TYLPCLD 146 (207)
Q Consensus 87 vI~~~~~~-----------e~lEr~~Fdi~~~~~~~~~~~~~~~~~~~i~~eiRa~l~qI~~s~----~~Lp~L~ 146 (207)
.++.+..+ .+.|+|..++...+...+++ ..+-.+.+.+.|++.+.+|...+ .++|+++
T Consensus 86 ~F~ekr~kk~WF~~~~~e~v~WE~W~I~v~v~~~~~~~e--r~~~r~~~~~~L~~~l~~Ii~~vn~~kdhIPpIt 158 (163)
T PF07855_consen 86 QFYEKRRKKSWFVGSGEEEVPWEQWTINVTVATPRTESE--RQKVREAVEDSLREALFKIIEIVNRHKDHIPPIT 158 (163)
T ss_pred EEEeecccccccccCCcccccceEEEEEEEEEcCCCchH--HHHHHHHHHHHHHHHHHHHHHHHCcCcccCCCCC
Confidence 88776433 37799999998866432211 22334566778899999887654 5677775
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=95.10 E-value=1.1 Score=38.53 Aligned_cols=170 Identities=21% Similarity=0.312 Sum_probs=97.3
Q ss_pred HHHHHHHhhhhhhhccC--------CCCCCcc-hhhhhcCCccccccCHhHHHHHHHHHHHHHHHHHcCccc----eEEE
Q 028572 20 VSEFFGYAANSILYNRG--------VYPEESF-VKVKKYGLPMLLTEDEGVKSFIANLTAQLSEWLEAGKLQ----RVVL 86 (207)
Q Consensus 20 v~efLe~aih~ILy~Rg--------iYP~~~F-~~~r~y~l~v~~sr~p~l~~YI~~~l~~v~~~L~~g~v~----kl~l 86 (207)
|.+|+.-+.|-||--|- ......+ ..-+-||+-+ -..|+ +...++.|...+... -+++
T Consensus 1 I~~F~~Kaa~iIl~SR~~~~~~~~~~~~~~~~~~~nkWFNL~~--~e~~~-------~~~~l~~w~~~~~~~~~~pPlvI 71 (233)
T PF10033_consen 1 IQNFFLKAAQIILQSRLNLSPSSSSSSSSSSSRKRNKWFNLEI--DESDE-------LREELKRWRSCSDLESRLPPLVI 71 (233)
T ss_pred ChHHHHHHHHHheeeccccCCCcccccccCCCCCCCccEeecC--CCcHH-------HHHHHHHhhhcccccCCCCCEEE
Confidence 46899999999999998 1222222 4566788766 23333 455667777633332 2333
Q ss_pred EEE-e---------------------------CCCcceeEEEeeeccccccccccccCCcCCHHHHHHHHHHHHHHHHhh
Q 028572 87 VIM-S---------------------------KATKEVLERWNFSIETDNEVVEKGVSREKSDKEIMREIQAIMRQIASS 138 (207)
Q Consensus 87 vI~-~---------------------------~~~~e~lEr~~Fdi~~~~~~~~~~~~~~~~~~~i~~eiRa~l~qI~~s 138 (207)
-|+ + +.+..+||||++.++....... ..........+-+.+-=.+|-|-+.
T Consensus 72 ei~Ld~~~l~~~~~l~l~d~~g~~~~v~~~~~~~~~ivLERW~i~~~~~~~~~~-~~~~~~~l~~vYK~~ivLfRSLys~ 150 (233)
T PF10033_consen 72 EIYLDTRQLSSNQSLVLKDDDGKRWDVCKGRSKKSEIVLERWLIELDSSSSPPS-PSDSGPELPTVYKRSIVLFRSLYSL 150 (233)
T ss_pred EEEEecCCCCCCCceEecCCCCceeeecccccCCCcEEEEEEEEEEecCCCCCC-ccccchhHHHHHHHHHHHHHHHHHH
Confidence 222 1 1245688999999982111111 1111234556666666666677777
Q ss_pred hhcCCC------C----CCCceEEEEEEecCCCC--CCC-------ccccCCcccccCCceeeeeeeecCceeeeeEEEE
Q 028572 139 ITYLPC------L----DETCVFDVLAYTDKDVA--VPF-------TWIESDPKLIANPQMVKLHSFDTKIHKVDTLVSY 199 (207)
Q Consensus 139 ~~~Lp~------L----~~~ctF~vlv~t~~~~~--~p~-------~Wi~sd~~~i~n~~~v~lrsfsT~~h~v~~~V~y 199 (207)
...||. + -..+.|.+..-.-.... .+. +-++++.. .-+...+..+.|.+-.+...|+|
T Consensus 151 ~RlLPA~kl~~~l~~~~~~~~~l~i~~Ri~~g~~~~~~~g~~~ls~p~~~~~~~---~~~~~~f~pv~Tp~G~L~isV~Y 227 (233)
T PF10033_consen 151 TRLLPAYKLFRRLAKSSSSSSSLSIGYRISDGSPPILSKGRIGLSKPIIPSESN---HMEQYSFGPVETPLGSLCISVSY 227 (233)
T ss_pred HHhChHHHHHHHhhhccCCCCcceeEEEEecCCcccccCCcccccccccCCCCC---ceeEEEECCcccCCccEEEEEEe
Confidence 777773 2 02346666655542110 001 11111111 22578899999999999999999
Q ss_pred ecC
Q 028572 200 KND 202 (207)
Q Consensus 200 ~~~ 202 (207)
|.+
T Consensus 228 R~~ 230 (233)
T PF10033_consen 228 RTD 230 (233)
T ss_pred cCC
Confidence 974
No 7
>KOG4493 consensus Uncharacterized conserved protein [Function unknown]
Probab=91.56 E-value=1.5 Score=37.49 Aligned_cols=140 Identities=17% Similarity=0.199 Sum_probs=89.5
Q ss_pred HHHHHHHHhhhhhhhccCC----CCCC---cchhhh-------hcCCccccccCHhHHHHHHHHHHHHHHHHHcCc---c
Q 028572 19 IVSEFFGYAANSILYNRGV----YPEE---SFVKVK-------KYGLPMLLTEDEGVKSFIANLTAQLSEWLEAGK---L 81 (207)
Q Consensus 19 ~v~efLe~aih~ILy~Rgi----YP~~---~F~~~r-------~y~l~v~~sr~p~l~~YI~~~l~~v~~~L~~g~---v 81 (207)
=+.|-..+.+|++||.|.+ |-.+ +|..+. ...++.-.+...+|+.=|+..+.+.+.||++.. +
T Consensus 16 qv~eaV~~ifh~vLlhR~vgkf~y~~~~~~s~GtVg~kdvdce~iDiTYV~~~s~EL~~kl~~~i~qF~~~ir~~~~~g~ 95 (219)
T KOG4493|consen 16 QVTEAVTCIFHTVLLHREVGKFVYGVELHRSFGTVGAKDVDCEFIDITYVRCVSAELNEKLDEKIAQFIDTIRNEAGAGV 95 (219)
T ss_pred ccchhhhhHHHHHHHHHhhhheEecceeEEEeccccccccceeEEEEEEEEechHHHHHHHHHHHHHHHHHHHhCCCCCc
Confidence 3677888899999999975 3322 222221 233344468889999999999999999998744 4
Q ss_pred ceEEEEEEeC---------CCcceeEEEeeeccccccccccccCCcCC--HHHHHHHHHHHHHHHHhhhhcCCCCCCCce
Q 028572 82 QRVVLVIMSK---------ATKEVLERWNFSIETDNEVVEKGVSREKS--DKEIMREIQAIMRQIASSITYLPCLDETCV 150 (207)
Q Consensus 82 ~kl~lvI~~~---------~~~e~lEr~~Fdi~~~~~~~~~~~~~~~~--~~~i~~eiRa~l~qI~~s~~~Lp~L~~~ct 150 (207)
..+.|-++.+ +..-+.|.|...++.......++.+.-.+ .+.+.+.. --+-+....-++||..|...-
T Consensus 96 gQi~L~FYekskK~~Wf~~~e~ipWEqW~l~l~vl~~~~~~e~q~~rs~vs~~l~ekv-~~i~E~~Nr~~y~pk~ptq~e 174 (219)
T KOG4493|consen 96 GQISLEFYEKSKKKRWFFKDETIPWEQWTLHLDVLEEESEDERQYCRSHVSDLLEEKV-EQIVEAMNRRSYLPKMPTQSE 174 (219)
T ss_pred ceEeeeeeecccCCCCCcCCCCccceeEEEEEEEeecccccccHHHHHHHHHHHHHHH-HHHHHHhhhhccCcCCchhhh
Confidence 5689999987 34567899998888766533222110000 11122211 123345567789999998777
Q ss_pred EEEEEEecC
Q 028572 151 FDVLAYTDK 159 (207)
Q Consensus 151 F~vlv~t~~ 159 (207)
|...-.|.-
T Consensus 175 ~~~iF~t~~ 183 (219)
T KOG4493|consen 175 SDNIFDTPF 183 (219)
T ss_pred cchhccCCc
Confidence 766644443
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=80.16 E-value=33 Score=30.44 Aligned_cols=145 Identities=14% Similarity=0.199 Sum_probs=62.0
Q ss_pred cceehhhHHHHHHHHHHHhhhhhhhccCCCCCCcchhhhhcCCccccccCHh-----------------HHHHHHHHHHH
Q 028572 9 DIITLRGSAAIVSEFFGYAANSILYNRGVYPEESFVKVKKYGLPMLLTEDEG-----------------VKSFIANLTAQ 71 (207)
Q Consensus 9 ~~itl~~s~~~v~efLe~aih~ILy~RgiYP~~~F~~~r~y~l~v~~sr~p~-----------------l~~YI~~~l~~ 71 (207)
..+|.+|..++++|+|.+ |||||+=-|-- ++.-+.|--...++.+.. +-+=+++++..
T Consensus 53 g~vtqd~ccrfV~ElLK~----iLYQRqQiPlp-YeQL~~f~~k~pq~~d~~~kk~~~~~~~~~kKcqq~L~eLE~vl~h 127 (264)
T PF06581_consen 53 GPVTQDGCCRFVCELLKH----ILYQRQQIPLP-YEQLAFFYRKSPQAKDDVRKKVSFSTEQSNKKCQQALQELESVLSH 127 (264)
T ss_dssp S---HHHHHHHHHHHHHH----HHHHTTSSSS--HHHHT-----------------------HHHHHHHHHHHHHHHHHH
T ss_pred CccccchhHHHHHHHHHH----HHhhhhcCCCh-HHHHHHHHhcCcccccccccccccccchhhHHHHHHHHHHHHHHHH
Confidence 357888999999998774 89999988762 222111111111211111 22223344444
Q ss_pred HHHHHHcCccceEEEEEEeCCCcceeEEEeeeccccccccccccCCcCCHHHHHHHHHHHHHHHHhhhhcCCC--CCCCc
Q 028572 72 LSEWLEAGKLQRVVLVIMSKATKEVLERWNFSIETDNEVVEKGVSREKSDKEIMREIQAIMRQIASSITYLPC--LDETC 149 (207)
Q Consensus 72 v~~~L~~g~v~kl~lvI~~~~~~e~lEr~~Fdi~~~~~~~~~~~~~~~~~~~i~~eiRa~l~qI~~s~~~Lp~--L~~~c 149 (207)
+...-....|.++.+.+=. .---+-|-|..|+.-..... .+.+. ....=+|..+|.|..++.|=-. .|---
T Consensus 128 Le~lFs~t~Vp~VLILLGg-t~~SPKE~YeInl~~l~~~s-----~e~sl-st~~clRkLfRsLf~aD~Fse~~~~Pl~~ 200 (264)
T PF06581_consen 128 LEQLFSLTLVPRVLILLGG-TAVSPKEFYEINLERLVPNS-----KEQSL-STAVCLRKLFRSLFTADAFSELQAPPLMG 200 (264)
T ss_dssp HHHHHHHS---EEEEEESS--SSS-SEEEEEE-TTS-------------S-HHHHHHHHHHHHHHHTTTT---S-----E
T ss_pred HHHHHhcCccceEEEEecC-ccCCcceeEEEcchhhcccc-----ccccc-ccHHHHHHHHHHHHcccchhhccCCCccc
Confidence 4444445667777665543 33347799999986433211 11122 1223466667777666544321 22222
Q ss_pred eEEEEEEecCCCCCCCccc
Q 028572 150 VFDVLAYTDKDVAVPFTWI 168 (207)
Q Consensus 150 tF~vlv~t~~~~~~p~~Wi 168 (207)
| -|++....|.. .+|-
T Consensus 201 T-iVmv~~hRdcg--~dWF 216 (264)
T PF06581_consen 201 T-IVMVQGHRDCG--SDWF 216 (264)
T ss_dssp E-EEEEEEECCC----SSS
T ss_pred e-EEEEEcCCCCC--cccc
Confidence 3 45566655543 4565
No 9
>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=52.63 E-value=4.6 Score=31.43 Aligned_cols=49 Identities=22% Similarity=0.407 Sum_probs=33.1
Q ss_pred ehhhHHHHHHHHHHHhhhhhhhccCCCCCCcc-hhhhhcCCccccccCHh
Q 028572 12 TLRGSAAIVSEFFGYAANSILYNRGVYPEESF-VKVKKYGLPMLLTEDEG 60 (207)
Q Consensus 12 tl~~s~~~v~efLe~aih~ILy~RgiYP~~~F-~~~r~y~l~v~~sr~p~ 60 (207)
+-+...+.+.++|..-+=.|...||.=|++.| +.+++||+|++.|..+.
T Consensus 66 ~~~~r~~~l~~l~~~~~P~iIvt~~~~~p~~l~e~a~~~~ipll~t~~~t 115 (127)
T PF02603_consen 66 DEEERKERLEKLFSYNPPCIIVTRGLEPPPELIELAEKYNIPLLRTPLST 115 (127)
T ss_dssp -HHHHCCHHHHHCTTT-S-EEEETTT---HHHHHHHHHCT--EEEESS-H
T ss_pred CHHHHHHHHHHHhCCCCCEEEEECcCCCCHHHHHHHHHhCCcEEEcCCcH
Confidence 33444567888999999999999999877766 66999999999998865
No 10
>PF04386 SspB: Stringent starvation protein B; InterPro: IPR007481 Escherichia coli stringent starvation protein B (SspB), is thought to enhance the specificity of degradation of tmRNA-tagged proteins by the ClpXP protease. The tmRNA tag, also known as ssrA, is an 11-aa peptide added to the C terminus of proteins stalled during translation, targets proteins for degradation by ClpXP and ClpAP. SspB is a cytoplasmic protein that specifically binds to residues 1-4 and 7 of the tag. Binding of SspB enhances degradation of tagged proteins by ClpX, and masks sequence elements important for ClpA interactions, inhibiting degradation by ClpA []. However, more recent work has cast doubt on the importance of SspB in wild-type cells []. SspB is encoded in an operon whose synthesis is stimulated by carbon, amino acid, and phosphate starvation. SspB may play a special role during nutrient stress, for example by ensuring rapid degradation of the products of stalled translation, without causing a global increase in degradation of all ClpXP substrates [].; PDB: 2NYS_A 2QAZ_D 2QAS_A 1OX9_A 1OX8_A 1YFN_C 1TWB_B 1OU9_C 1OU8_B 1ZSZ_B ....
Probab=52.56 E-value=33 Score=27.72 Aligned_cols=52 Identities=23% Similarity=0.238 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHhhhhcCCCCCCCceEEEEEEecCC-CCCCCccccCCcccccC
Q 028572 125 MREIQAIMRQIASSITYLPCLDETCVFDVLAYTDKD-VAVPFTWIESDPKLIAN 177 (207)
Q Consensus 125 ~~eiRa~l~qI~~s~~~Lp~L~~~ctF~vlv~t~~~-~~~p~~Wi~sd~~~i~n 177 (207)
...|||+.+.+-..++... +|.+|||-|.+-|+.. ..+|..-.+.+++.+.|
T Consensus 8 py~lrav~~w~l~~~~~~~-~d~~~tpyI~v~t~~pgV~vP~~~~~~~~~ivln 60 (155)
T PF04386_consen 8 PYLLRAVYEWILEDVAKAG-LDNDHTPYITVDTDYPGVQVPDQLVEQDGQIVLN 60 (155)
T ss_dssp HHHHHHHHHHHHHHHCCCT-HHTT--EEEEEETTSTT-BSSGGGHCBTTEEEEE
T ss_pred HHHHHHHHHHHHHHHHhcC-CCCCCeEEEEEEeCCCCCCCCHHHhccCCcEEEE
Confidence 4578999999877776666 8999999999999865 56677666688886554
No 11
>PF10259 Rogdi_lz: Rogdi leucine zipper containing protein
Probab=51.10 E-value=1.2e+02 Score=26.73 Aligned_cols=34 Identities=24% Similarity=0.407 Sum_probs=24.0
Q ss_pred hcCCCCCCCceEEEEEEecCC--------CCCCCccccCCcc
Q 028572 140 TYLPCLDETCVFDVLAYTDKD--------VAVPFTWIESDPK 173 (207)
Q Consensus 140 ~~Lp~L~~~ctF~vlv~t~~~--------~~~p~~Wi~sd~~ 173 (207)
.|-|+||.+++|++.|.-.+= ...+.+|-+.|+.
T Consensus 159 ~F~P~Lp~~ls~~~~I~~~~Lvl~~~~L~~~~~~p~~~i~~~ 200 (273)
T PF10259_consen 159 SFCPPLPPDLSFDFYIQDNELVLDLRQLEPVTPKPWCEIDSS 200 (273)
T ss_pred ccCCCCCcceEEEEEEecceeeeeeeeeEEccccccccccCC
Confidence 488999999999877765431 1235789888754
No 12
>COG0768 FtsI Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]
Probab=49.79 E-value=33 Score=33.45 Aligned_cols=47 Identities=21% Similarity=0.182 Sum_probs=42.4
Q ss_pred hhcCCccccccCHhHHHHHHHHHHHHHHHHHcCccceEEEEEEeCCCccee
Q 028572 47 KKYGLPMLLTEDEGVKSFIANLTAQLSEWLEAGKLQRVVLVIMSKATKEVL 97 (207)
Q Consensus 47 r~y~l~v~~sr~p~l~~YI~~~l~~v~~~L~~g~v~kl~lvI~~~~~~e~l 97 (207)
-+-|-.|+.|-|..|+.++.++|..... ...++..+++.|+.|+|+|
T Consensus 235 ~~~G~dv~LTID~~lQ~~~e~~l~~~~~----~~~~~g~~vv~dpktGeIL 281 (599)
T COG0768 235 PKDGKDVQLTIDLRLQKAAEEALDKAVA----NKAKGGAAVVLDPKTGEIL 281 (599)
T ss_pred CCCCCceEEEecHHHHHHHHHHHHHHHh----cCCcceEEEEEeCCCCcEE
Confidence 5678999999999999999999998766 7889999999999999875
No 13
>KOG3874 consensus Uncharacterized conserved protein [Function unknown]
Probab=44.91 E-value=2.8e+02 Score=26.38 Aligned_cols=132 Identities=16% Similarity=0.242 Sum_probs=79.1
Q ss_pred cccCHhHHHHHHHHHHHHHHHHHcCccceEEEEEEeCC-CcceeEEEeeeccccccccccccCCcCCHHHHHHHHHHHHH
Q 028572 55 LTEDEGVKSFIANLTAQLSEWLEAGKLQRVVLVIMSKA-TKEVLERWNFSIETDNEVVEKGVSREKSDKEIMREIQAIMR 133 (207)
Q Consensus 55 ~sr~p~l~~YI~~~l~~v~~~L~~g~v~kl~lvI~~~~-~~e~lEr~~Fdi~~~~~~~~~~~~~~~~~~~i~~eiRa~l~ 133 (207)
+--+|++-+|...+|.. .....|.-=+|.+.++..+ +.-+||-|+.+.....+ ...+...++-.-+--.|+
T Consensus 55 I~d~pEV~~e~K~altg--~~p~vgl~lcvEisLkT~eGd~m~LE~W~L~~~ateg------~~~k~~~~~Ynrms~lLk 126 (504)
T KOG3874|consen 55 IDDLPEVSAELKSALTG--SYPPVGLTLCVEISLKTPEGDLMPLEAWILSSSATEG------TDDKSRNELYNRMSTLLK 126 (504)
T ss_pred hhchHHHHHHHHHHhcc--CCCccCcceEEEEEEecCCCCeeeeehheeccccccC------chhHHHHHHHHHHHHHHH
Confidence 45688888888777721 2222233335556666554 23578999999873211 112445566666766777
Q ss_pred HHHhhhhcCCC--C---CCCceEEEEEEecCCCCCCCccccCCcccccCCceeeeeeeecCceeeeeEEEEec
Q 028572 134 QIASSITYLPC--L---DETCVFDVLAYTDKDVAVPFTWIESDPKLIANPQMVKLHSFDTKIHKVDTLVSYKN 201 (207)
Q Consensus 134 qI~~s~~~Lp~--L---~~~ctF~vlv~t~~~~~~p~~Wi~sd~~~i~n~~~v~lrsfsT~~h~v~~~V~y~~ 201 (207)
.+.++...-|. | .+...+-|+.+.-=+ .++. ++ +-++.+.|++...+|.+-++.+.++||-
T Consensus 127 Sli~~tR~TPayrLsrkq~~~ey~I~yriyf~--~~q~---s~--lGeG~ktvkiG~l~T~vG~i~ls~aYRt 192 (504)
T KOG3874|consen 127 SLIVSTRMTPAYRLSRKQQHLEYFIIYRIYFE--NDQS---SD--LGEGKKTVKIGELVTKVGNISLSLAYRT 192 (504)
T ss_pred HHHHHhccChhhhhhhhcCCcceEEEEEEEec--Cccc---cc--cccCceeEEeeeeeeeeccEEEEEeeee
Confidence 77776666663 2 243455554433211 1111 11 2234579999999999999999999996
No 14
>PRK05428 HPr kinase/phosphorylase; Provisional
Probab=37.23 E-value=62 Score=29.34 Aligned_cols=78 Identities=22% Similarity=0.348 Sum_probs=56.1
Q ss_pred eehhhHHHHHHHHHHHhhhhhhhccCCCCCCcc-hhhhhcCCccccccCHhHHHHHHHHHHHHHHHHHc-CccceEEEEE
Q 028572 11 ITLRGSAAIVSEFFGYAANSILYNRGVYPEESF-VKVKKYGLPMLLTEDEGVKSFIANLTAQLSEWLEA-GKLQRVVLVI 88 (207)
Q Consensus 11 itl~~s~~~v~efLe~aih~ILy~RgiYP~~~F-~~~r~y~l~v~~sr~p~l~~YI~~~l~~v~~~L~~-g~v~kl~lvI 88 (207)
++-+.-...+..++..-+-.|...||.-|++.| +..++||+|++.|..+. ...++.+..-+...|.. -.++-..+.|
T Consensus 66 l~~~~r~~~~~~l~~~~~P~iIvt~~~~~p~~l~~~a~~~~ipll~t~~~t-~~~i~~l~~~L~~~la~~~~iHg~~v~V 144 (308)
T PRK05428 66 LSEEERKERLKKLFSLEPPCIIVTRGLEPPPELLEAAKEAGIPLLRTPLST-TRLISKLTNYLDRKLAPRTSVHGVLVDI 144 (308)
T ss_pred CCHHHHHHHHHHHhCCCCCEEEEECcCCCCHHHHHHHHHcCCcEEEeCCcH-HHHHHHHHHHHHHHhhhcceeeeEEEEE
Confidence 455566778899999999999999999999865 66999999999999854 55555555555555533 2344444443
Q ss_pred E
Q 028572 89 M 89 (207)
Q Consensus 89 ~ 89 (207)
.
T Consensus 145 ~ 145 (308)
T PRK05428 145 Y 145 (308)
T ss_pred C
Confidence 3
No 15
>PF14242 DUF4342: Domain of unknown function (DUF4342)
Probab=35.20 E-value=46 Score=24.35 Aligned_cols=28 Identities=18% Similarity=0.406 Sum_probs=22.9
Q ss_pred HhHHHHHHHHHHHHHHHHHcCccceEEE
Q 028572 59 EGVKSFIANLTAQLSEWLEAGKLQRVVL 86 (207)
Q Consensus 59 p~l~~YI~~~l~~v~~~L~~g~v~kl~l 86 (207)
..++..-+++++.+++++.+|.+.|+.+
T Consensus 9 e~~~~~g~~~~~~iK~li~kGNv~Ri~I 36 (84)
T PF14242_consen 9 EEFQVKGEELVDKIKELIKKGNVTRIII 36 (84)
T ss_pred ceeeecHHHHHHHHHHHHHhcCeEEEEE
Confidence 3445556889999999999999999865
No 16
>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=33.20 E-value=16 Score=30.25 Aligned_cols=51 Identities=10% Similarity=0.176 Sum_probs=37.4
Q ss_pred CCCCCcchhhhhcCCccccccCHhHHHHHHHHHHHHHHHHHcCccceEEEE
Q 028572 37 VYPEESFVKVKKYGLPMLLTEDEGVKSFIANLTAQLSEWLEAGKLQRVVLV 87 (207)
Q Consensus 37 iYP~~~F~~~r~y~l~v~~sr~p~l~~YI~~~l~~v~~~L~~g~v~kl~lv 87 (207)
+.|+-.|-..+.-++-+.++|-|....+..++.+.+.+|+.+..++++++.
T Consensus 55 ~~~~~~iy~~~~~~i~vl~~~~p~~~~~~~~f~~~l~~~~~~~g~~~vi~l 105 (219)
T PF09754_consen 55 LSPPLEIYYSEDSKILVLQGRSPIPPGRWYEFAEELLDWIKSFGVKEVIVL 105 (219)
T ss_dssp EB-SEEEEEEECTTEEEEEESSE--SCGHHHHHHHHHHHHHHTTECEEEEE
T ss_pred eccceEEEEECCCCEEEEEecCCCCchHHHHHHHHHHHHHHHcCCCEEEEE
Confidence 344444434444458888999999999999999999999999999998853
No 17
>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=33.13 E-value=23 Score=23.40 Aligned_cols=18 Identities=17% Similarity=0.361 Sum_probs=14.8
Q ss_pred ccCHhHHHHHHHHHHHHH
Q 028572 56 TEDEGVKSFIANLTAQLS 73 (207)
Q Consensus 56 sr~p~l~~YI~~~l~~v~ 73 (207)
++..+|.+||+++|..|.
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 455679999999998875
No 18
>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=32.92 E-value=68 Score=23.54 Aligned_cols=38 Identities=16% Similarity=0.232 Sum_probs=31.7
Q ss_pred cccCHhHHHHHHHHHHHHH-HHHHcCccceEEEEEEeCC
Q 028572 55 LTEDEGVKSFIANLTAQLS-EWLEAGKLQRVVLVIMSKA 92 (207)
Q Consensus 55 ~sr~p~l~~YI~~~l~~v~-~~L~~g~v~kl~lvI~~~~ 92 (207)
.+-..+|++||..++.... ..+.+..++++.|.+.+++
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 4456889999999999977 5578999999999998764
No 19
>cd00552 RaiA RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site. RaiA is also thought to counteract miscoding at the A site thus reducing translation errors. The RaiA fold structurally resembles the double-stranded RNA-binding domain (dsRBD).
Probab=27.36 E-value=2.1e+02 Score=20.13 Aligned_cols=36 Identities=8% Similarity=0.351 Sum_probs=28.3
Q ss_pred cccCHhHHHHHHHHHHHHHHHHHcCccceEEEEEEeCC
Q 028572 55 LTEDEGVKSFIANLTAQLSEWLEAGKLQRVVLVIMSKA 92 (207)
Q Consensus 55 ~sr~p~l~~YI~~~l~~v~~~L~~g~v~kl~lvI~~~~ 92 (207)
+.-.+.+++||.+-+..+.... ..+..+.+.+....
T Consensus 9 ~~~t~al~~~i~~k~~kl~r~~--~~i~~~~V~l~~~~ 44 (93)
T cd00552 9 IEVTDALREYVEEKLEKLEKYF--DRIISVDVVLSVEK 44 (93)
T ss_pred ccCCHHHHHHHHHHHHHHHHhc--CCCceEEEEEEEec
Confidence 4567999999999999977777 66777777776544
No 20
>PF07607 DUF1570: Protein of unknown function (DUF1570); InterPro: IPR011464 This entry represents hypothetical proteins confined to bacteria.
Probab=24.42 E-value=37 Score=26.75 Aligned_cols=16 Identities=25% Similarity=0.567 Sum_probs=14.3
Q ss_pred hhhhhhhccCCCCCCc
Q 028572 27 AANSILYNRGVYPEES 42 (207)
Q Consensus 27 aih~ILy~RgiYP~~~ 42 (207)
++|+|+|..|+-|...
T Consensus 9 a~HQl~~N~Gl~~r~~ 24 (128)
T PF07607_consen 9 ATHQLAFNTGLHPRLA 24 (128)
T ss_pred HHHHHHHHccccccCC
Confidence 8999999999998764
No 21
>PRK15105 peptidoglycan synthase FtsI; Provisional
Probab=23.37 E-value=1.8e+02 Score=28.38 Aligned_cols=47 Identities=19% Similarity=0.181 Sum_probs=37.6
Q ss_pred hcCCccccccCHhHHHHHHHHHHHHHHHHHcCccceEEEEEEeCCCccee
Q 028572 48 KYGLPMLLTEDEGVKSFIANLTAQLSEWLEAGKLQRVVLVIMSKATKEVL 97 (207)
Q Consensus 48 ~y~l~v~~sr~p~l~~YI~~~l~~v~~~L~~g~v~kl~lvI~~~~~~e~l 97 (207)
.-|-.|+.+-|+.|++++.++|....+ +....+-++++.|+.|+++|
T Consensus 226 ~~G~~v~LTID~~lQ~~ae~~l~~~~~---~~~~~~ga~Vvmdp~TG~IL 272 (578)
T PRK15105 226 QAAHNLALSIDERLQALVYRELNNAVA---FNKAESGSAVLVDVNTGEVL 272 (578)
T ss_pred CCCCcEEEEeCHHHHHHHHHHHHHHHH---HhCCCeEEEEEEECCCCcEE
Confidence 457789999999999999999876432 34455789999999999876
No 22
>COG3814 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.58 E-value=2.2e+02 Score=23.18 Aligned_cols=37 Identities=8% Similarity=0.143 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHHhhhhcCCCCCCCceEEEEEEecCC
Q 028572 123 EIMREIQAIMRQIASSITYLPCLDETCVFDVLAYTDKD 160 (207)
Q Consensus 123 ~i~~eiRa~l~qI~~s~~~Lp~L~~~ctF~vlv~t~~~ 160 (207)
-.++++|++++++-+-++.-. ||.+.-|=|..-|+..
T Consensus 11 laqealrgvvkkvL~kva~~g-Lp~dhh~yItf~T~ap 47 (157)
T COG3814 11 LAQEALRGVVKKVLAKVAATG-LPGDHHFYITFLTGAP 47 (157)
T ss_pred HHHHHHHHHHHHHHHHHhhcC-CCCCcEEEEEEecCCC
Confidence 357789999999888777655 9999999888888753
No 23
>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=21.60 E-value=2.1e+02 Score=21.62 Aligned_cols=46 Identities=17% Similarity=0.362 Sum_probs=32.1
Q ss_pred cccCHhHHHHHHHHHHHHHHHHHcCccceEEEEEEeCCCcceeEEEeeecc
Q 028572 55 LTEDEGVKSFIANLTAQLSEWLEAGKLQRVVLVIMSKATKEVLERWNFSIE 105 (207)
Q Consensus 55 ~sr~p~l~~YI~~~l~~v~~~L~~g~v~kl~lvI~~~~~~e~lEr~~Fdi~ 105 (207)
++.+..|-+|++.+...-. ++.-+.+.|.++|.+..++ =||.|.=-
T Consensus 59 ~~~~~~l~~W~~~~~~~~~----~~~~~~~~I~lld~~~~~~-~~w~~~~a 104 (134)
T PF06841_consen 59 VDESSDLWDWFNAINNGES----NSARKDISIELLDSDGKPV-ARWNFRNA 104 (134)
T ss_pred ccCcHHHHHHHHHHhcccc----ccccceEEEEEECCCCCEE-EEEEEEeE
Confidence 5667888888876655422 2237789999999887544 49998743
No 24
>TIGR02071 PBP_1b penicillin-binding protein 1B. Bacterial that synthesize a cell wall of peptidoglycan (murein) generally have several transglycosylases and transpeptidases for the task. This family consists of a particular bifunctional transglycosylase/transpeptidase in E. coli and other Proteobacteria, designated penicillin-binding protein 1B.
Probab=21.44 E-value=1.9e+02 Score=29.15 Aligned_cols=50 Identities=20% Similarity=0.114 Sum_probs=38.6
Q ss_pred hcCCccccccCHhHHHHHHHHHHHHHHHHHcC---ccceEEEEEEeCCCccee
Q 028572 48 KYGLPMLLTEDEGVKSFIANLTAQLSEWLEAG---KLQRVVLVIMSKATKEVL 97 (207)
Q Consensus 48 ~y~l~v~~sr~p~l~~YI~~~l~~v~~~L~~g---~v~kl~lvI~~~~~~e~l 97 (207)
.-|+.|+-+-||.++++..+++..-.+-+.++ .--.-++++.|..|++++
T Consensus 367 ~~G~~I~TTLD~~lQ~~ae~al~~~~~~~~~~~~~~~~~gA~Vv~Dp~TGeIl 419 (730)
T TIGR02071 367 LSGLRIFTTLDPVSQSAAEQAVQETIPALKKKKKLPDLEAAMVVTDRFTGEVR 419 (730)
T ss_pred cCCcEEEEecCHHHHHHHHHHHHHHHHhhhccccccccceeEEEEECCCCcEE
Confidence 55889999999999999999998765555432 123568888999998764
No 25
>TIGR02074 PBP_1a_fam penicillin-binding protein, 1A family. Bacterial that synthesize a cell wall of peptidoglycan (murein) generally have several transglycosylases and transpeptidases for the task. This family consists of bifunctional transglycosylase/transpeptidase penicillin-binding proteins (PBP). In the Proteobacteria, this family includes PBP 1A but not the paralogous PBP 1B (TIGR02071). This family also includes related proteins, often designated PBP 1A, from other bacterial lineages.
Probab=20.89 E-value=1.7e+02 Score=28.18 Aligned_cols=50 Identities=16% Similarity=0.043 Sum_probs=38.0
Q ss_pred hcCCccccccCHhHHHHHHHHHHHHHHHHHc--CccceEEEEEEeCCCccee
Q 028572 48 KYGLPMLLTEDEGVKSFIANLTAQLSEWLEA--GKLQRVVLVIMSKATKEVL 97 (207)
Q Consensus 48 ~y~l~v~~sr~p~l~~YI~~~l~~v~~~L~~--g~v~kl~lvI~~~~~~e~l 97 (207)
.=|..|+-+-|+.|++.+.+++..-...... +.-....+++.|+.|++++
T Consensus 219 ~~G~~I~tTID~~lQ~~ae~~l~~~~~~~~~~~~~~~~~a~Vv~d~~TG~Il 270 (530)
T TIGR02074 219 TGGLKIYTTLDLDMQKAAEKVLNNGLREAGRRANDDLQAALVAIDPDTGAVR 270 (530)
T ss_pred cCCcEEEEeeCHHHHHHHHHHHHhhhhccccccccccceeEEEEECCCCeEE
Confidence 3478899999999999999999875544332 1124678999999999765
No 26
>TIGR02073 PBP_1c penicillin-binding protein 1C. This subfamily of the penicillin binding proteins includes the member from E. coli designated penicillin-binding protein 1C. Members have both transglycosylase and transpeptidase domains and are involved in forming cross-links in the late stages of peptidoglycan biosynthesis. All members of this subfamily are presumed to have the same basic function.
Probab=20.70 E-value=2e+02 Score=29.05 Aligned_cols=46 Identities=13% Similarity=0.249 Sum_probs=38.4
Q ss_pred ccccccCHhHHHHHHHHHHHHHHHHHcCccceEEEEEEeCCCccee
Q 028572 52 PMLLTEDEGVKSFIANLTAQLSEWLEAGKLQRVVLVIMSKATKEVL 97 (207)
Q Consensus 52 ~v~~sr~p~l~~YI~~~l~~v~~~L~~g~v~kl~lvI~~~~~~e~l 97 (207)
.|+-+-|+.+++.+.+++.+-...+..+.+....+++.|..|++++
T Consensus 243 ~I~tTiD~~lQ~~ae~~l~~~~~~~~~~~~~~~a~vv~D~~TG~Il 288 (727)
T TIGR02073 243 VIVSTLDADLQRRLEELARRYLSALRPRGISNLAILVVDNRSGAVL 288 (727)
T ss_pred EEEEeeCHHHHHHHHHHHHHHHHhcCccccceEEEEEEECCCCcEE
Confidence 4899999999999999998866666555556889999999999765
No 27
>cd08641 DNA_pol_gammaA Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria. DNA polymerase gamma (Pol gamma), 5'-3' polymerase domain (Pol gammaA). Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gammaA, and several bacteriophage polymerases including those from odd-nu
Probab=20.14 E-value=3.9e+02 Score=25.42 Aligned_cols=89 Identities=9% Similarity=0.148 Sum_probs=52.2
Q ss_pred hhhcCCccccccCHhHHHHHHHHHHHHHHHHHcCcc-ceEEEEEEeCCCcceeEEEeeeccccccccccccCCcCCHHHH
Q 028572 46 VKKYGLPMLLTEDEGVKSFIANLTAQLSEWLEAGKL-QRVVLVIMSKATKEVLERWNFSIETDNEVVEKGVSREKSDKEI 124 (207)
Q Consensus 46 ~r~y~l~v~~sr~p~l~~YI~~~l~~v~~~L~~g~v-~kl~lvI~~~~~~e~lEr~~Fdi~~~~~~~~~~~~~~~~~~~i 124 (207)
+-..|-||+=|. -+||.-++-.+..+|.+..+ .+++|.|+|. . +|++.... .....+
T Consensus 316 rsaIN~pIQGSA----ADiiKlaMV~m~~~l~~~~i~aRmlLqVHDE----L----~feV~eed----------~yr~al 373 (425)
T cd08641 316 TSRINWVVQSSA----VDYLHLMLVSMRWLIEKYDIDARFCISIHDE----V----RYLVKEED----------KYRAAL 373 (425)
T ss_pred HHHhcccchhhH----HHHHHHHHHHHHHHHHhcCCCceEEEEECeE----e----eeeccHHH----------HHHHHH
Confidence 334455555443 47888999999999987554 4788888752 2 35543211 122333
Q ss_pred HHHHHHHHHHHHhhh-hcCCCCCCCceEEEEEE
Q 028572 125 MREIQAIMRQIASSI-TYLPCLDETCVFDVLAY 156 (207)
Q Consensus 125 ~~eiRa~l~qI~~s~-~~Lp~L~~~ctF~vlv~ 156 (207)
-.++...+.+-..+. --|..||+.|.|==.|.
T Consensus 374 alqi~nlltram~a~~lg~~dlPqs~affs~vd 406 (425)
T cd08641 374 ALQITNLLTRAMFAQKLGINDLPQSVAFFSAVD 406 (425)
T ss_pred HHHHHHHHHHHHHHHHhccccCCcchhhhhhhh
Confidence 445555555533322 23578999999944443
Done!