Query 002338
Match_columns 934
No_of_seqs 287 out of 1050
Neff 6.2
Searched_HMMs 46136
Date Thu Mar 28 21:47:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002338.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002338hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2030 Predicted RNA-binding 100.0 4E-166 1E-170 1414.6 52.7 780 2-932 1-780 (911)
2 COG1293 Predicted RNA-binding 100.0 1.4E-88 2.9E-93 799.5 49.4 553 2-684 1-564 (564)
3 PF05833 FbpA: Fibronectin-bin 100.0 4.1E-60 8.9E-65 551.0 24.5 409 7-553 1-434 (455)
4 PF05670 DUF814: Domain of unk 99.9 6.3E-28 1.4E-32 220.4 9.7 90 562-653 1-90 (90)
5 COG1293 Predicted RNA-binding 97.6 0.0013 2.8E-08 79.4 16.0 121 347-515 256-377 (564)
6 KOG3272 Predicted coiled-coil 97.5 0.00031 6.6E-09 71.3 8.2 89 565-656 10-102 (207)
7 PRK01103 formamidopyrimidine/5 96.0 0.26 5.5E-06 54.6 16.9 51 238-291 156-209 (274)
8 PRK10445 endonuclease VIII; Pr 95.4 0.23 5E-06 54.6 13.6 50 239-291 153-205 (263)
9 KOG2030 Predicted RNA-binding 94.5 0.01 2.3E-07 71.6 0.2 97 831-927 139-252 (911)
10 PRK14811 formamidopyrimidine-D 94.5 0.79 1.7E-05 50.7 14.7 50 239-291 145-197 (269)
11 PRK13945 formamidopyrimidine-D 94.0 1.6 3.6E-05 48.5 16.0 50 239-291 166-218 (282)
12 TIGR00577 fpg formamidopyrimid 93.8 1.4 3.1E-05 48.8 15.0 50 239-291 157-209 (272)
13 COG0266 Nei Formamidopyrimidin 92.8 4.3 9.3E-05 44.9 16.4 42 247-291 168-209 (273)
14 PF06831 H2TH: Formamidopyrimi 90.9 0.52 1.1E-05 43.6 5.8 50 239-291 25-77 (92)
15 PRK14810 formamidopyrimidine-D 90.4 0.56 1.2E-05 51.9 6.6 51 238-291 155-208 (272)
16 PF00416 Ribosomal_S13: Riboso 86.2 1.8 3.9E-05 41.2 6.2 49 238-289 11-59 (107)
17 COG0099 RpsM Ribosomal protein 85.9 1.1 2.4E-05 43.2 4.5 47 240-289 15-61 (121)
18 CHL00137 rps13 ribosomal prote 85.1 0.96 2.1E-05 44.1 3.8 48 239-289 14-61 (122)
19 PRK05179 rpsM 30S ribosomal pr 84.6 0.84 1.8E-05 44.5 3.2 48 239-289 14-61 (122)
20 TIGR03631 bact_S13 30S ribosom 81.7 1.2 2.7E-05 42.8 3.0 47 239-288 12-58 (113)
21 PTZ00134 40S ribosomal protein 79.8 2.3 5.1E-05 43.1 4.4 46 240-288 28-73 (154)
22 PRK04053 rps13p 30S ribosomal 77.6 2.4 5.2E-05 42.8 3.7 47 239-288 22-68 (149)
23 TIGR03629 arch_S13P archaeal r 74.9 4.1 8.9E-05 40.9 4.5 47 240-289 19-65 (144)
24 PRK04184 DNA topoisomerase VI 67.8 31 0.00067 42.0 10.4 51 238-291 256-307 (535)
25 COG1730 GIM5 Predicted prefold 57.5 2.2E+02 0.0048 28.8 13.7 38 395-432 7-44 (145)
26 TIGR01052 top6b DNA topoisomer 49.8 92 0.002 37.6 10.1 51 238-291 247-301 (488)
27 KOG0407 40S ribosomal protein 46.7 62 0.0013 30.9 6.3 24 586-610 21-45 (139)
28 PF13077 DUF3909: Protein of u 44.8 17 0.00037 32.9 2.3 28 582-609 64-92 (108)
29 COG1389 DNA topoisomerase VI, 39.7 73 0.0016 37.8 6.9 53 237-292 255-312 (538)
30 KOG1832 HIV-1 Vpr-binding prot 39.7 25 0.00054 44.3 3.3 9 668-676 1356-1364(1516)
31 PF09602 PhaP_Bmeg: Polyhydrox 32.4 5.9E+02 0.013 26.4 12.5 34 499-532 123-156 (165)
32 PF06099 Phenol_hyd_sub: Pheno 30.6 90 0.0019 26.8 4.3 31 93-125 9-39 (59)
33 COG1671 Uncharacterized protei 29.7 43 0.00093 33.9 2.7 70 569-640 47-120 (150)
34 PF04568 IATP: Mitochondrial A 23.8 3E+02 0.0065 26.2 7.0 26 378-403 74-99 (100)
35 KOG0994 Extracellular matrix g 23.5 1.4E+03 0.03 30.8 14.3 41 404-444 1457-1498(1758)
36 PF03993 DUF349: Domain of Unk 22.6 4.1E+02 0.0089 22.9 7.4 14 353-366 6-19 (77)
37 PF12925 APP_E2: E2 domain of 21.5 8.7E+02 0.019 25.8 10.5 15 411-425 96-110 (193)
38 PF07889 DUF1664: Protein of u 21.4 8E+02 0.017 24.3 11.8 45 378-422 52-96 (126)
No 1
>KOG2030 consensus Predicted RNA-binding protein [General function prediction only]
Probab=100.00 E-value=4.5e-166 Score=1414.57 Aligned_cols=780 Identities=49% Similarity=0.736 Sum_probs=662.2
Q ss_pred ccCCCCHHHHHHHHHHHhhhcCCceeEEEecCCCEEEEEEeeCCCCccCCCCceEEEEEeccceEEeecccCCCCCCCcH
Q 002338 2 VKVRMNTADVAAEVKCLRRLIGMRCSNVYDLSPKTYIFKLMNSSGVTESGESEKVLLLMESGVRLHTTAYARDKKNTPSG 81 (934)
Q Consensus 2 mK~rms~lDv~a~v~EL~~L~G~RI~nIY~~~~~t~llk~~~~~g~~~~~~~~k~~LliesG~RiHlT~~~~~k~~~Ps~ 81 (934)
|||||++|||.+.|+||+.|.|+||+|||++++++|+|+|.++ . .|+++||+|||+|.+.++++.+||+
T Consensus 1 mk~r~~tldi~~~v~elk~L~g~r~~niYdi~~ktyl~K~~~~---------d--~ll~e~GvRih~T~~~~ek~~tpSG 69 (911)
T KOG2030|consen 1 MKQRFNTLDIAATVAELKPLVGMRVNNIYDISNKTYLIKFSNK---------D--ILLVESGVRIHLTQFDQEKSTTPSG 69 (911)
T ss_pred CcchhHHHHHHHHHHHHHHhhhhhhhceeeccccEEEEEecCC---------c--eEEeeccceeeeeeccccCCCCcch
Confidence 8999999999999999999999999999999999999999987 1 7999999999999999999999999
Q ss_pred HHHHHHHHccCCceeEEEeeCCCeEEEEEEeeCCceEEEEEEEecCceEEEEcCCCcEEeeecccccCCCccccccCCcc
Q 002338 82 FTLKLRKHIRTRRLEDVRQLGYDRIILFQFGLGMNAHYVILELYAQGNILLTDSEFTVLTLLRSHRDDDKGVAIMSRHRY 161 (934)
Q Consensus 82 F~m~LRKhL~g~RL~~V~Qlg~DRIV~~~f~~G~~~~~LIvEL~grgNIILtD~~~~IL~~lR~~~~~~~~~~i~~g~~Y 161 (934)
|||+|||||+..||++|+|+|+||||+|+||.|+.+++||||||++|||||||.+++||.+||.|+++......+++++|
T Consensus 70 F~~kLRKhik~kRledv~Q~g~DRivvlqfG~g~~~~~lvLE~~d~GNviLtdqe~~i~~llrv~~dd~~~~~~~~rer~ 149 (911)
T KOG2030|consen 70 FSMKLRKHIKEKRLEDVRQVGFDRIVVLQFGTGDDEGYLVLEFFDRGNVLLTDQELRILQLLRVRTDDSESSRSASRERF 149 (911)
T ss_pred HHHHHHHHHhHhhhchhhhcCcceEEEEEecCCCccceEEEEecCCCceEEecccceeeeEEeeeeccccchhhhhhhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999988777889999999
Q ss_pred cCccccccccCChhhhHHhhccCCCCCCCCCCCccCCCCCcccccccccCCCCCCCccccccccCCCCCCCccCCchhHH
Q 002338 162 PTEICRVFERTTASKLHAALTSSKEPDANEPDKVNEDGNNVSNASKENLGGQKGGKSFDLSKNSNKNSNDGARAKQPTLK 241 (934)
Q Consensus 162 p~~~~~~~~p~~~~kl~~~l~~~~~~~~~~~~~~~~n~~~~~~~~~e~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~lk 241 (934)
|+..+..+..-+..++.... +. .+|. .....+.++.
T Consensus 150 ~~s~~e~~~~k~~~~le~s~----------------dl-------------------k~~~---------~~~q~g~~~~ 185 (911)
T KOG2030|consen 150 DFSAKERNEMKSVKKLEKSG----------------DL-------------------KALE---------PKDQNGITLE 185 (911)
T ss_pred chhhhhhhhccccchhhhcc----------------hH-------------------HHhh---------ccCccccchh
Confidence 98775544322222221100 00 0000 1112346788
Q ss_pred HHHhhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHHHHHHHHhhcCCCcceEEEEecccCCCCCCC
Q 002338 242 TVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKFEDWLQDVISGDIVPEGYILMQNKHLGKDHP 321 (934)
Q Consensus 242 ~~L~~~~g~gp~laeei~~ragl~~~~~~~~~~~l~~~~~~~L~~al~~~~~~l~~l~~~~~~p~gyi~~~~~~~~~~~~ 321 (934)
.+|...+++||...+|++..+++.+..+.+....+.+.++..|.++++.+++|+.++.++...|.|||.+.....+.+
T Consensus 186 ~il~~~~~~g~sk~k~~v~~~~~~~~sKsse~~~~~~~~i~~l~e~v~~~eE~~~elit~~~~~~Gyi~~~k~~~~~s-- 263 (911)
T KOG2030|consen 186 SILHIETKEGPSKIKHIVLDMKKGQLSKSSENIKLFDSEIKKLQEAVKDQEEEDRELITGKLGSKGYILEEKEKKPIS-- 263 (911)
T ss_pred hhhhhhccCCCccchhhhhhhcccccccccccccccchhhHHHHHHHHHHHHHHHHHHhCCCcccchhHHhhcccCCC--
Confidence 999999999999999999999998877755555677888999999999999999999999988999997665322211
Q ss_pred CCCCCCCCccceeeeeecccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002338 322 PTESGSSTQIYDEFCPLLLNQFRSREFVKFETFDAALDEFYSKIESQRAEQQHKAKEDAAFHKLNKIHMDQENRVHTLKQ 401 (934)
Q Consensus 322 ~~~~~~~~~~~~~f~P~~l~q~~~~~~~~f~sf~~AlDeffs~~e~qk~~~~~~~~e~~~~kkLek~~~~qe~ri~~L~~ 401 (934)
.....|.+||| .+.+|...++..|++|++|+|+|||.+++|+..++....+..+.+||++++++|+++++.|++
T Consensus 264 -----~~~~~y~~f~p-~~~~fKs~~~k~fetf~ea~Def~S~IEsqk~~lr~~~~E~qa~kKld~vr~Dq~~rvq~Lqq 337 (911)
T KOG2030|consen 264 -----TKEFIYDEFHP-LGVQFKSEPVKKFETFNEAVDEFFSTIESQKSELRVKNQELQAEKKLDKVRKDQKERVQELQQ 337 (911)
T ss_pred -----ccceeeccccc-cccccccchhhhccchhhHHHHHHHHHhhhhHHHHHHhhHhHHHhhhhcchhhHHHHHHHHHH
Confidence 22468999999 778999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCcccccccccccCCeEEEeccCCCCCccc
Q 002338 402 EVDRSVKMAELIEYNLEDVDAAILAVRVALANRMSWEDLARMVKEERKAGNPVAGLIDKLYLERNCMSLLLSNNLDEMDD 481 (934)
Q Consensus 402 e~e~~~~~aeLI~~Nl~~V~~~i~~v~~a~a~g~~W~~i~~~i~~~~~~g~pvA~~I~~l~l~~n~itl~L~d~~d~~d~ 481 (934)
.++.++++|+||+.|..+|+.+|.+|++++++||+|.+|++|++.++++|||||..|.+++++.|++++.|.|+++|+||
T Consensus 338 ~qe~~~~kAelIe~N~eLVe~~il~I~s~la~~m~W~dieKLik~eqKkGn~vAk~i~~l~l~~n~~t~~L~d~~dd~~d 417 (911)
T KOG2030|consen 338 VQELNRRKAELIEPNPELVEAAILAIQSALAQQMDWKDIEKLIKSEQKKGNPVAKSIDKLKLEKNEATLRLKDPEDDNDD 417 (911)
T ss_pred HHHHHHHHHHhccCCHHHHHHHHHHHHHHHHccCCcHhHHHHHHHHHhcCchHhhhhhHHHHhhhhheeecCCcccccch
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998777
Q ss_pred cccCCCceEEEeCCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhchhhHHHhhhcccccCce
Q 002338 482 EEKTLPVEKVEVDLALSAHANARRWYELKKKQESKQEKTITAHSKAFKAAEKKTRLQILQEKTVANISHMRKVHWFEKFN 561 (934)
Q Consensus 482 ~~~~~~~v~I~LDl~lSa~~NA~~yy~k~KK~~~K~ekt~~a~~~alk~aE~k~~~~L~~~~~~~~l~~iRk~~wfEKF~ 561 (934)
+..+.+.+.|+||++|||++||++||.++|+++.|+++|..++++||++++.|++++|++.+++..|.++|+++||||||
T Consensus 418 e~k~~e~~~VeiDLslsA~aNArr~y~~kk~aa~K~kKT~~a~eKAlK~~e~Ki~q~lk~~~~~~~i~k~Rk~~wFEKf~ 497 (911)
T KOG2030|consen 418 EKKSSEVIVVEIDLSLSAFANARRYYEMKKEAAEKIKKTVDASEKALKSAERKIEQQLKQVKTVSRIKKIRKVYWFEKFH 497 (911)
T ss_pred hhccccceeeeeeccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhcccceeehhee
Confidence 77788889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeccCCeEEEecCChhhHHHHHHHhcCCCCEEEEecCCCCcEEEEecCCCCCCCCHHHHHHHHHHHHHhccccCCCCcc
Q 002338 562 WFISSENYLVISGRDAQQNEMIVKRYMSKGDVYVHADLHGASSTVIKNHRPEQPVPPLTLNQAGCFTVCHSQAWDSKMVT 641 (934)
Q Consensus 562 wFiSSdGylVivGRDa~QNE~LvkKya~~~Diw~HAdi~GAShVIIKn~~~g~~ip~~tL~eAA~lAa~ySkAW~sk~V~ 641 (934)
|||||+|||||+||||||||+||+|||+|+|||||||+||||||||||+ ++.+|||.||.|||+||+|||+||++++|+
T Consensus 498 wFiSSEg~LVi~GrdaqQnEllvkky~~~~DiY~had~~gaSsviIkN~-~~~eipp~TL~eAg~ma~~~S~aWdakvvs 576 (911)
T KOG2030|consen 498 WFISSEGYLVIGGRDAQQNELLVKKYLEPGDIYVHADLHGASSVIIKNP-PKTEIPPKTLEEAGSMALCYSKAWDAKVVS 576 (911)
T ss_pred EEEecCcEEEEcCCChhhhhHHHHhhCCCCCeEEecccCCCceEEEeCC-CCCCCChhhHHHHHHHHhHHhhhhcccccc
Confidence 9999999999999999999999999999999999999999999999995 789999999999999999999999999999
Q ss_pred eEEEEecccccccCCCCceeccCcEEEeeeccccCCCCceeEEEEEEEecccccccccccccccCccCCCCcccccCCCC
Q 002338 642 SAWWVYPHQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLIMGFGLLFRLDESSLGSHLNERRVRGEEEGMDDFEDSGHHK 721 (934)
Q Consensus 642 sa~wV~~~QVSKtapsGeyL~~GsFmIrGkKnflpp~~L~mg~gilf~~de~~~~~h~~~r~~~~~~~~~~~~~~~~~~~ 721 (934)
+|||||++|||||||||||||+||||||||||||||++|+|||||||+||++++++|.++|+++.+++.+.+.+ . +
T Consensus 577 saWwv~~dqVSKtaptgeyL~~GSFmIrgkkN~lpp~~LvmG~GlLfrldes~~E~~~~~r~~~~eee~~~~~e-~--e- 652 (911)
T KOG2030|consen 577 SAWWVYPDQVSKTAPTGEYLPTGSFMIRGKKNFLPPHQLVMGLGLLFRLDESSIERHLGERKVEEEEEKEEDEE-P--E- 652 (911)
T ss_pred cceEEecccccccCCCCccccccceEEecccCCCCchhheecceeEEEeccchhhhhhhhHHHHHHHhhhcccc-h--h-
Confidence 99999999999999999999999999999999999999999999999999999999999999988887664310 0 0
Q ss_pred CCCccccccCcCCCccccccCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCCchhhhhcccCCCCCCcchhhcccc
Q 002338 722 ENSDIESEKDDTDEKPVAESLSVPNSAHPAPSHTNASNVDSHEFPAEDKTISNGIDSKIFDIARNVAAPVTPQLEDLIDR 801 (934)
Q Consensus 722 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 801 (934)
..++. ++ .. +++. ++ +.++ ..+++.
T Consensus 653 ----~~ee~---------~s---------~~-----~e~~---------------~~------------~~s~-~e~~~~ 677 (911)
T KOG2030|consen 653 ----LMEEV---------ES---------KT-----SEIP---------------EE------------VISN-DEFPVN 677 (911)
T ss_pred ----hhhhc---------cc---------cc-----ccCC---------------cc------------cccc-cccccc
Confidence 00000 00 00 0000 00 0000 001111
Q ss_pred cccccccccCCCccCccccccccccccccccccccccCCcccchHHHHHhhcCCCCCCCCchhhhhhhccCCCCCCCccc
Q 002338 802 ALGLGSASISSTKHGIETTQFDLSEEDKHVERTATVRDKPYISKAERRKLKKGQGSSVVDPKVEREKERGKDASSQPESI 881 (934)
Q Consensus 802 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~kk~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 881 (934)
.+ ......| .......++++.+.++|..+|+++.+...+....++..-.....++-..
T Consensus 678 ev--~~~~~~G--------------------k~~~~~~~~~~~~~~~~~~~k~~s~~~~~~n~~~~k~~~~e~~~~~is~ 735 (911)
T KOG2030|consen 678 EV--KGREKTG--------------------KNVQEESKTFIGKGPKREKKKVQSASKEEDNVGRAKQRIGESSVQPISD 735 (911)
T ss_pred cc--cccccCC--------------------cchhhhhhhhhhcCccchhhhccccccchhhhhHHHHhhhhcccccccc
Confidence 00 0001111 1223457889999999999999888765553332222211111111111
Q ss_pred ccccccCCCCCCCcccchhhhhhhhhcCCChHHHHHHHHHHhccCCccccC
Q 002338 882 VRKTKIEGGKISRGQKGKLKKMKEKYGDQDEEERNIRMALLAVSTLTCTIG 932 (934)
Q Consensus 882 ~~~~~~~~~~~~rg~~~k~kk~~~ky~dqdee~r~~~m~~l~~~~~~~~~~ 932 (934)
-+.+ .-+.+||||||||||| |+||||+||+|+|++|+++|+ -+-+
T Consensus 736 ep~~---~~~~~rg~kgklkkmk--y~dQd~~er~~r~~~l~~~~k-ek~~ 780 (911)
T KOG2030|consen 736 EPSN---KNQVKRGQKGKLKKMK--YADQDEDERELRMELLKSSGK-EKQQ 780 (911)
T ss_pred CCcc---hHHHHHhhhhhhhhhh--hcccCchHHHHHHHhcccccc-cccc
Confidence 0111 1356899999999999 999999999999999999998 4433
No 2
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=100.00 E-value=1.4e-88 Score=799.48 Aligned_cols=553 Identities=29% Similarity=0.423 Sum_probs=409.5
Q ss_pred ccCCCCHHHHHHHHHHHh-hhcCCceeEEEecCCCEEEEEEeeCCCCccCCCCceEEEEEeccce--EEeecccCCCCCC
Q 002338 2 VKVRMNTADVAAEVKCLR-RLIGMRCSNVYDLSPKTYIFKLMNSSGVTESGESEKVLLLMESGVR--LHTTAYARDKKNT 78 (934)
Q Consensus 2 mK~rms~lDv~a~v~EL~-~L~G~RI~nIY~~~~~t~llk~~~~~g~~~~~~~~k~~LliesG~R--iHlT~~~~~k~~~ 78 (934)
||++||++|++++|.||+ .|.|+||.||||+..+++.|.++.++ . .+..|+++.|.| ||+|.+.+++|..
T Consensus 1 mk~~~~~ldl~a~~~EL~~~l~g~ri~kIyq~~~~~~~l~i~~~~------~-~~~~li~~~~~~~~i~lT~~~~~~p~~ 73 (564)
T COG1293 1 MKMKFDSLDLAAIVEELKEQLEGGRIDKIYQPGEDELILLLRFGG------K-GRKLLLSEHPVRSRIHLTKKPKENPAL 73 (564)
T ss_pred CCcchhhhhHHHHHHHHHhhhhhhhhhhhcCCCCceEEEEEEcCC------C-CceEEEEecCCcceEEeCCCCcCCCCC
Confidence 899999999999999999 79999999999999999999999884 2 467788888866 9999999999999
Q ss_pred CcHHHHHHHHHccCCceeEEEeeCCCeEEEEEEe---eCCc-eEEEEEEEecC-ceEEEEcCCCcEEeeecccccCCCcc
Q 002338 79 PSGFTLKLRKHIRTRRLEDVRQLGYDRIILFQFG---LGMN-AHYVILELYAQ-GNILLTDSEFTVLTLLRSHRDDDKGV 153 (934)
Q Consensus 79 Ps~F~m~LRKhL~g~RL~~V~Qlg~DRIV~~~f~---~G~~-~~~LIvEL~gr-gNIILtD~~~~IL~~lR~~~~~~~~~ 153 (934)
||+|||.|||||+|++|++|+|+|+||||+|+|+ .|+. .++|++|+||+ |||||||++++||+++|++++. +|
T Consensus 74 p~~F~~~LRK~l~g~~i~~i~Q~~~DRIl~~~f~~~~~~~~~~~eL~~ei~g~~gNiil~d~~~~Ii~~~r~v~~~--~R 151 (564)
T COG1293 74 PSSFAMLLRKHLKGARIEKIEQLGFDRILELKFKKDEIGDKIIVELFLEIMGKHGNLILVDEERKIIEALRHVTFS--DR 151 (564)
T ss_pred CChHHHHHHHHhccCceEeEEecCCceEEEEEEeccCCCCceeeeeehhhccccceEEEEcCCCeeeeeeeecccc--ce
Confidence 9999999999999999999999999999999998 2333 67888888888 9999999999999999999987 56
Q ss_pred ccccCCcccCccccccccCChhh--hHHhhccCCCCCCCCCCCccCCCCCcccccccccCCCCCCCccccccccCCCCCC
Q 002338 154 AIMSRHRYPTEICRVFERTTASK--LHAALTSSKEPDANEPDKVNEDGNNVSNASKENLGGQKGGKSFDLSKNSNKNSND 231 (934)
Q Consensus 154 ~i~~g~~Yp~~~~~~~~p~~~~k--l~~~l~~~~~~~~~~~~~~~~n~~~~~~~~~e~~~~~~~~~~~d~~~~~~~~~~~ 231 (934)
.|.+|..|..||...-+|.+... +...+
T Consensus 152 ~i~pG~~Y~~Pp~~~~~p~~~~~~~~~~~~-------------------------------------------------- 181 (564)
T COG1293 152 TIKPGEIYILPPAQLKNPYEQSEEDFKELQ-------------------------------------------------- 181 (564)
T ss_pred eecCCCcccCCcccCCChhhcChHHHHHHH--------------------------------------------------
Confidence 99999999766654323432221 11100
Q ss_pred CccCCchhHHHHHhhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHHHHHHHHhhcCCCcceEEEEe
Q 002338 232 GARAKQPTLKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKFEDWLQDVISGDIVPEGYILM 311 (934)
Q Consensus 232 ~~~~~~~~lk~~L~~~~g~gp~laeei~~ragl~~~~~~~~~~~l~~~~~~~L~~al~~~~~~l~~l~~~~~~p~gyi~~ 311 (934)
...+..+++++..++|+||.+++++|.|+|+++..++. ++..+.+..+..+ +.+|+..+ .|..|. .
T Consensus 182 --~~~~~~~~~~~~~~~g~~~~~a~el~~rag~~~~~~~~---~~~~~~~~~v~~~---~~~~~~~~-----~~~~~~-~ 247 (564)
T COG1293 182 --LNSGADIVRLLARFLGLGGLLAEELLSRAGLDKKVPAK---DLFEEEIKKVREA---LEELLNPL-----KPNYYY-K 247 (564)
T ss_pred --hccchHHHHHHHHhcCCCHHHHHHHHHhcCCCcCCchh---hhhHHHHHHHHHH---HHhhhhcc-----ccCcee-e
Confidence 01256788999999999999999999999999887643 3566677666555 44444433 132222 1
Q ss_pred cccCCCCCCCCCCCCCCCccceeeeeecccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002338 312 QNKHLGKDHPPTESGSSTQIYDEFCPLLLNQFRSREFVKFETFDAALDEFYSKIESQRAEQQHKAKEDAAFHKLNKIHMD 391 (934)
Q Consensus 312 ~~~~~~~~~~~~~~~~~~~~~~~f~P~~l~q~~~~~~~~f~sf~~AlDeffs~~e~qk~~~~~~~~e~~~~kkLek~~~~ 391 (934)
. ..+.+..| +..|.+.. .+||+++|+||....................++|++....
T Consensus 248 ~-----------------~~~~~~~p--~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~kl~~~i~~ 304 (564)
T COG1293 248 D-----------------EKYLDVVP--LKAYADLE----KLFNEALDEKFERDKIKQLASELEKKLEKELKKLENKLEK 304 (564)
T ss_pred e-----------------cccccccc--ccccchhh----HHHHHHHHHHhhhhhHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence 1 12334444 44442211 1799999999988543333223445555666778888888
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCcccccccccccCCeEEEe
Q 002338 392 QENRVHTLKQEVDRSVKMAELIEYNLEDVDAAILAVRVALANRMSWEDLARMVKEERKAGNPVAGLIDKLYLERNCMSLL 471 (934)
Q Consensus 392 qe~ri~~L~~e~e~~~~~aeLI~~Nl~~V~~~i~~v~~a~a~g~~W~~i~~~i~~~~~~g~pvA~~I~~l~l~~n~itl~ 471 (934)
|++.++.++..++.++++|+||++|++.|+..+..|+.+...+ |+.|.. .......|+. +.+. -..+...
T Consensus 305 ~~~~~~~~~~~~~~~r~~g~ll~an~~~i~~~~~~v~~~~~~~--~~~i~i---~l~~~~~~~~--~~~~---~~~~~~k 374 (564)
T COG1293 305 QEDELEELEKAAEELRQKGELLYANLQLIEEGLKSVRLADFYG--NEEIKI---ELDKSKTPSE--NAQR---YFKKYKK 374 (564)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhehhhhcc--ccceee---ccCcCcccch--hhHH---Hhhhhhh
Confidence 8999999898999999999999999999998666555443332 111100 0000000000 0000 0000000
Q ss_pred ccCCCCCccccccCCCceEEEeCCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhchhhHHHh
Q 002338 472 LSNNLDEMDDEEKTLPVEKVEVDLALSAHANARRWYELKKKQESKQEKTITAHSKAFKAAEKKTRLQILQEKTVANISHM 551 (934)
Q Consensus 472 L~d~~d~~d~~~~~~~~v~I~LDl~lSa~~NA~~yy~k~KK~~~K~ekt~~a~~~alk~aE~k~~~~L~~~~~~~~l~~i 551 (934)
| +...+.+++.++..+|+..||++.+++.+|... ..+++.+. ++.+++.+.+ ......
T Consensus 375 l--------------k~~~~~~~~~~~~~~~~~~y~e~~~~~lek~~~-~~~ieei~---ee~ie~~~~~----~~k~~~ 432 (564)
T COG1293 375 L--------------KGAKVNLDRQLSELKEAIAYYESAKTALEKAEG-KKAIEEIR---EELIEEGLLK----SKKKKR 432 (564)
T ss_pred c--------------cCceeehhhhhhhhHHHHHHHHHHHHHHHhccc-hhhHHHHH---HHHHHHHHhh----hhHHhh
Confidence 0 113455555666666666666665555554443 22222221 1112211111 233455
Q ss_pred hhcccccCceEEeccCCeEEEecCChhhHHHHHHHhcCCCCEEEEecCCCCcEEEEecCCCCCCCCHHHHHHHHHHHHHh
Q 002338 552 RKVHWFEKFNWFISSENYLVISGRDAQQNEMIVKRYMSKGDVYVHADLHGASSTVIKNHRPEQPVPPLTLNQAGCFTVCH 631 (934)
Q Consensus 552 Rk~~wfEKF~wFiSSdGylVivGRDa~QNE~LvkKya~~~Diw~HAdi~GAShVIIKn~~~g~~ip~~tL~eAA~lAa~y 631 (934)
|++.||++|+||+||+||+|++||||.|||.||+||++++||||||+.+||||||||+ ++..+|+.||.+||.|||||
T Consensus 433 kkk~~~ek~~~~~ss~Gf~vi~Grna~qNe~l~~k~~~~~DlwfHa~~~~gshvvik~--~~~~~~e~ti~eAA~~Aa~~ 510 (564)
T COG1293 433 KKKEWFEKFRWFVSSDGFLVIGGRNAKQNEELVKKYAEKDDLWFHADDIPGSHVVIKT--EGKEPSEETILEAAQLAASY 510 (564)
T ss_pred hhhhhcccceeeeccCCeEEEEecCcccchHHHHhhcccCcEEEEccCCCCCeEEEeC--CCCCCChHHHHHHHHHHHHh
Confidence 6789999999999999999999999999999999999999999999999999999999 47789999999999999999
Q ss_pred ccccCCCCcc-eEEEEecccccccCCCCceeccCcEEEeeeccccCCCCceeEE
Q 002338 632 SQAWDSKMVT-SAWWVYPHQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLIMGF 684 (934)
Q Consensus 632 SkAW~sk~V~-sa~wV~~~QVSKtapsGeyL~~GsFmIrGkKnflpp~~L~mg~ 684 (934)
|+||.++.|+ ++|||++.||+|+|+||+||++|+|||||++||+...+|.+++
T Consensus 511 Ska~~~~~v~vd~t~vk~vqv~K~a~~G~vl~~g~~~I~~k~~~~~~~~lk~~~ 564 (564)
T COG1293 511 SKAWKSGLVPVDYTWVKPVQVPKGAKSGEVLYKGQKTIRGKRDYITIVKLKLAV 564 (564)
T ss_pred chHhhcCCCceEEEEEcccccCCCCCCceEEecCcEEEEEccccccccccccCC
Confidence 9999999775 9999999999999999999999999999999999999988763
No 3
>PF05833 FbpA: Fibronectin-binding protein A N-terminus (FbpA); InterPro: IPR008616 This family consists of the N-terminal region of the prokaryotic fibronectin-binding protein, the C-terminal region is IPR008532 from INTERPRO. Fibronectin binding is considered to be an important virulence factor in streptococcal infections. Fibronectin is a dimeric glycoprotein that is present in a soluble form in plasma and extracellular fluids; it is also present in a fibrillar form on cell surfaces. Both the soluble and cellular forms of fibronectin may be incorporated into the extracellular tissue matrix. While fibronectin has critical roles in eukaryotic cellular processes, such as adhesion, migration and differentiation, it is also a substrate for the attachment of bacteria. The binding of pathogenic Streptococcus pyogenes and Staphylococcus aureus to epithelial cells via fibronectin facilitates their internalisation and systemic spread within the host [].; PDB: 3DOA_A 2ZBK_F 2HKJ_A 1Z5B_A 1Z5C_B 1MX0_F 1Z5A_A 1MU5_A 1Z59_A.
Probab=100.00 E-value=4.1e-60 Score=550.96 Aligned_cols=409 Identities=28% Similarity=0.443 Sum_probs=175.7
Q ss_pred CHHHHHHHHHHHh-hhcCCceeEEEecCCCEEEEEEeeCCCCccCCCCceEEEEEec---cceEEeecccCCCCCCCcHH
Q 002338 7 NTADVAAEVKCLR-RLIGMRCSNVYDLSPKTYIFKLMNSSGVTESGESEKVLLLMES---GVRLHTTAYARDKKNTPSGF 82 (934)
Q Consensus 7 s~lDv~a~v~EL~-~L~G~RI~nIY~~~~~t~llk~~~~~g~~~~~~~~k~~Llies---G~RiHlT~~~~~k~~~Ps~F 82 (934)
|++||+|+|.||+ .|+|+||.||||+++++|+|+|++++ ++.+|+|++ |+|||+|.+.+++|..|++|
T Consensus 1 D~l~l~a~~~El~~~l~g~~i~~i~q~~~~~~~l~~~~~~--------~~~~L~i~~~~~~~ri~lt~~~~~~~~~~~~f 72 (455)
T PF05833_consen 1 DGLDLRALVKELKKKLEGGRIDKIYQPDKRELLLKFRKPG--------GNHWLLISAHPSGPRIHLTEKPRENPKEPSPF 72 (455)
T ss_dssp -HHHHHHHHHHHGG-GTT-EEEEEEEEETTEEEEEEEETT--------EEEEEEEE--TTT-EEEEE-----------HH
T ss_pred CHHHHHHHHHHHHHhhcCCEEEEEEcCCCCEEEEEEEeCC--------CcEEEEEEEcCCCceeEecCCCCCCCCCCchH
Confidence 6899999999999 69999999999999999999999764 466788876 89999999999899999999
Q ss_pred HHHHHHHccCCceeEEEeeCCCeEEEEEEeeC-----CceEEEEEEEecC-ceEEEEcCCCcEEeeecccccC-CCcccc
Q 002338 83 TLKLRKHIRTRRLEDVRQLGYDRIILFQFGLG-----MNAHYVILELYAQ-GNILLTDSEFTVLTLLRSHRDD-DKGVAI 155 (934)
Q Consensus 83 ~m~LRKhL~g~RL~~V~Qlg~DRIV~~~f~~G-----~~~~~LIvEL~gr-gNIILtD~~~~IL~~lR~~~~~-~~~~~i 155 (934)
||.|||||+|+||++|+|+|+||||.|+|+.+ ...|+|||||||+ |||||||++++||+++|+++.. .+.|.|
T Consensus 73 ~~~Lrk~l~g~~i~~i~q~~~dRii~~~~~~~~~~~~~~~~~Li~El~g~~~NiiL~d~~~~Il~a~~~~~~~~~~~R~i 152 (455)
T PF05833_consen 73 CMLLRKHLRGARIVSIEQLGFDRIIEIEFESGDELGDDEKYRLIIELMGRHSNIILTDEDGKILDALRRVSFSQSRDREI 152 (455)
T ss_dssp HHHHHHHHTT-EEEEEEESTTSSEEEEEEEEE-TTS-EEEEEEEEE--GGG-EEEEEETT-BEEEESS-B---------B
T ss_pred HHHHHHHhCCCEEEEEEEcCCcEEEEEEeeccCcCCCceeEEEEEEEcCCcccEEEEcCCCeEEeehhhcCcccccceee
Confidence 99999999999999999999999999999976 3489999999999 9999999999999999999986 346899
Q ss_pred ccCCcccCccc-cccccCChhh---hHHhhccCCCCCCCCCCCccCCCCCcccccccccCCCCCCCccccccccCCCCCC
Q 002338 156 MSRHRYPTEIC-RVFERTTASK---LHAALTSSKEPDANEPDKVNEDGNNVSNASKENLGGQKGGKSFDLSKNSNKNSND 231 (934)
Q Consensus 156 ~~g~~Yp~~~~-~~~~p~~~~k---l~~~l~~~~~~~~~~~~~~~~n~~~~~~~~~e~~~~~~~~~~~d~~~~~~~~~~~ 231 (934)
.+|.+|.+|+. ....|.+.+. +.+.+.
T Consensus 153 ~~G~~Y~~Pp~~~~~~p~~~~~~~~~~~~l~------------------------------------------------- 183 (455)
T PF05833_consen 153 LPGEPYIPPPPQDKLDPLDLEEFEEFIELLK------------------------------------------------- 183 (455)
T ss_dssp STTSB---------B-CCC--H-HHHHHHHH-------------------------------------------------
T ss_pred ccCccccccccccCCCcccchhHHHHHHhhc-------------------------------------------------
Confidence 99999976664 2234443333 222210
Q ss_pred CccCCchhHHHHH-hhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHHHHHHHHhhcCCCcceEEEE
Q 002338 232 GARAKQPTLKTVL-GEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKFEDWLQDVISGDIVPEGYIL 310 (934)
Q Consensus 232 ~~~~~~~~lk~~L-~~~~g~gp~laeei~~ragl~~~~~~~~~~~l~~~~~~~L~~al~~~~~~l~~l~~~~~~p~gyi~ 310 (934)
....++.++| ..+.||||.+++|+|.++|++++.++. .++++++..|+.+ +..|+..+..+.+.|+.|+
T Consensus 184 ---~~~~~l~~~L~~~~~G~~~~la~ei~~ra~i~~~~~~~---~~~~~~~~~l~~~---~~~l~~~l~~~~~~p~l~~- 253 (455)
T PF05833_consen 184 ---KKEKTLVKALSKNFQGFGPELAEEILYRAGIDKNKKVE---ELSDEEIEKLFEA---IRELLNELEEGQFKPYLYY- 253 (455)
T ss_dssp ---CCG-BHHHHHHHHCTT--HHHHHHHHCCCTS-TTSBGG---G--HHHHCHHHHH---HHHHHHHHT---S----EE-
T ss_pred ---cCcccHHHHHHHHHHHhHHHHHHHHHHHhCCCCccccc---cchhhhHHHHHHH---HHHhhhhcccccCccEEEE-
Confidence 0223454444 456699999999999999999998764 5788888888877 6778888888876675554
Q ss_pred ecccCCCCCCCCCCCCCCCccceeeeeecccccccccccccccHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH
Q 002338 311 MQNKHLGKDHPPTESGSSTQIYDEFCPLLLNQFRSREFVKFETFDAALDEFYSKIES-QRAEQQHKAKEDAAFHKLNKIH 389 (934)
Q Consensus 311 ~~~~~~~~~~~~~~~~~~~~~~~~f~P~~l~q~~~~~~~~f~sf~~AlDeffs~~e~-qk~~~~~~~~e~~~~kkLek~~ 389 (934)
++ ..+..|+||++.++.+.....|+||++|||+||+..+. .++.+. .+.+.+++++.+
T Consensus 254 -~~----------------~~~~~f~~~~l~~~~~~~~~~f~s~~~ald~yf~~~~~~~~~~~~----~~~l~k~l~~~~ 312 (455)
T PF05833_consen 254 -DD----------------GKPKDFSPFPLKQYEELEVKEFDSFNEALDEYFSEKEEEERLEQK----KKRLEKKLEKKI 312 (455)
T ss_dssp -E---------------------EEESS--TT---S--EE-SSHHHHHHHHT----------------------------
T ss_pred -ec----------------CcccEEEEEeccccccccccCCCCHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHH
Confidence 43 24679999999888777788999999999999998643 333333 334445566666
Q ss_pred HHHHHHHHHHHH------HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCcccccccccc
Q 002338 390 MDQENRVHTLKQ------EVDRSVKMAELIEYNLEDVDAAILAVRVALANRMSWEDLARMVKEERKAGNPVAGLIDKLYL 463 (934)
Q Consensus 390 ~~qe~ri~~L~~------e~e~~~~~aeLI~~Nl~~V~~~i~~v~~a~a~g~~W~~i~~~i~~~~~~g~pvA~~I~~l~l 463 (934)
.+++++++.|++ ..+.++.+|+||++|++.+.. |++|.++.
T Consensus 313 ~klek~l~~l~~~~~~~~~~~~~~~~gelL~a~~~~i~~-----------g~~~~~l~---------------------- 359 (455)
T PF05833_consen 313 KKLEKKLEKLEEELEESEKAENYREYGELLLANLHQIKK-----------GMKWVELE---------------------- 359 (455)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhC-----------CCCEEEhh----------------------
Confidence 666666666654 446778899999999998874 99985553
Q ss_pred cCCeEEEeccCCCCCccccccCCCceEEEeCCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH--HHHHHHHh
Q 002338 464 ERNCMSLLLSNNLDEMDDEEKTLPVEKVEVDLALSAHANARRWYELKKKQESKQEKTITAHSKAFKAAEK--KTRLQILQ 541 (934)
Q Consensus 464 ~~n~itl~L~d~~d~~d~~~~~~~~v~I~LDl~lSa~~NA~~yy~k~KK~~~K~ekt~~a~~~alk~aE~--k~~~~L~~ 541 (934)
|++.+ ...++|+|||.+||++||++||++|||+++|.+++..+++.+.+.++. ....+++.
T Consensus 360 ----------~~~~~-------~~~i~I~Ld~~~s~~eNA~~yf~k~kK~k~k~~~~~~~i~~~~~el~~l~~~~~~l~~ 422 (455)
T PF05833_consen 360 ----------DFYEE-------GEEIEIPLDPSLSPSENAQKYFKKYKKLKRKIEKLEERIEEAEKELEYLESKLEQLEE 422 (455)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred ----------hhhcc-------CCceEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 32221 124899999999999999999999999988777777666554443332 12334555
Q ss_pred hhchhhHHHhhh
Q 002338 542 EKTVANISHMRK 553 (934)
Q Consensus 542 ~~~~~~l~~iRk 553 (934)
+.+..+|..+|.
T Consensus 423 a~~~~~l~~i~~ 434 (455)
T PF05833_consen 423 AEDLEELEEIRE 434 (455)
T ss_dssp ------------
T ss_pred cCCHHHHHHHHH
Confidence 556667776665
No 4
>PF05670 DUF814: Domain of unknown function (DUF814); InterPro: IPR008532 This domain occurs in proteins that have been annotated as Fibronectin/fibrinogen binding protein by similarity. This annotation comes from O34693 from SWISSPROT where the N-terminal region is involved in this activity []. Hence the activity of this C-terminal domain is unknown. This domain contains a conserved motif D/E-X-W/Y-X-H that may be functionally important.
Probab=99.95 E-value=6.3e-28 Score=220.43 Aligned_cols=90 Identities=32% Similarity=0.581 Sum_probs=81.9
Q ss_pred EEeccCCeEEEecCChhhHHHHHHHhcCCCCEEEEecCCCCcEEEEecCCCCCCCCHHHHHHHHHHHHHhccccCCCCcc
Q 002338 562 WFISSENYLVISGRDAQQNEMIVKRYMSKGDVYVHADLHGASSTVIKNHRPEQPVPPLTLNQAGCFTVCHSQAWDSKMVT 641 (934)
Q Consensus 562 wFiSSdGylVivGRDa~QNE~LvkKya~~~Diw~HAdi~GAShVIIKn~~~g~~ip~~tL~eAA~lAa~ySkAW~sk~V~ 641 (934)
||+||+||+||+|||++|||.|++||++++||||||+.+||||||||++ ..+.++.+|.+||+||||||+||..+...
T Consensus 1 wF~s~~g~~i~vGrn~~eNe~L~~k~~~~~D~wfH~~~~pg~hvil~~~--~~~~~~~~l~~AA~laa~~Ska~~~~~~v 78 (90)
T PF05670_consen 1 WFISSDGFKIIVGRNAKENEMLTKKYARPNDLWFHADDFPGPHVILRNN--PGDEPPPTLQEAAQLAASYSKAWKKGEKV 78 (90)
T ss_pred CEEecCCeEEEEeCCHHHHHHHHHHhhhhcceeEeccCCCCCEEEEECC--CCccchHHHHHHHHHHHHhCHhhccCCCe
Confidence 9999999999999999999999999999999999998888899999995 33344449999999999999999888877
Q ss_pred eEEEEecccccc
Q 002338 642 SAWWVYPHQVSK 653 (934)
Q Consensus 642 sa~wV~~~QVSK 653 (934)
.+||+..++|+|
T Consensus 79 ~V~yt~~k~v~K 90 (90)
T PF05670_consen 79 EVDYTQGKYVKK 90 (90)
T ss_pred EEEEeehHhccC
Confidence 789999999987
No 5
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=97.56 E-value=0.0013 Score=79.38 Aligned_cols=121 Identities=21% Similarity=0.237 Sum_probs=92.8
Q ss_pred cccccccHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 002338 347 EFVKFETFDAALDEFYSKI-ESQRAEQQHKAKEDAAFHKLNKIHMDQENRVHTLKQEVDRSVKMAELIEYNLEDVDAAIL 425 (934)
Q Consensus 347 ~~~~f~sf~~AlDeffs~~-e~qk~~~~~~~~e~~~~kkLek~~~~qe~ri~~L~~e~e~~~~~aeLI~~Nl~~V~~~i~ 425 (934)
+...|++++..+++||... ...++.+... .+.+++++.+..+++.++.++++.+.++..++......+.|-.-+.
T Consensus 256 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~l~~~~~kl~~~i~~~~~~~~~~~~~~~~~r~~g~ll~an~~ 331 (564)
T COG1293 256 PLKAYADLEKLFNEALDEKFERDKIKQLAS----ELEKKLEKELKKLENKLEKQEDELEELEKAAEELRQKGELLYANLQ 331 (564)
T ss_pred cccccchhhHHHHHHHHHHhhhhhHHHhHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456788888899999874 5555555544 3678888888888999999999999999999999988888876555
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHHcCCCcccccccccccCCeEEEeccCCCCCccccccCCCceEEEeCCCCCHHHHHHH
Q 002338 426 AVRVALANRMSWEDLARMVKEERKAGNPVAGLIDKLYLERNCMSLLLSNNLDEMDDEEKTLPVEKVEVDLALSAHANARR 505 (934)
Q Consensus 426 ~v~~a~a~g~~W~~i~~~i~~~~~~g~pvA~~I~~l~l~~n~itl~L~d~~d~~d~~~~~~~~v~I~LDl~lSa~~NA~~ 505 (934)
.|...+. .+.+.+++. .+.+.|++|+..++.+|+++
T Consensus 332 ~i~~~~~------------------------------------~v~~~~~~~--------~~~i~i~l~~~~~~~~~~~~ 367 (564)
T COG1293 332 LIEEGLK------------------------------------SVRLADFYG--------NEEIKIELDKSKTPSENAQR 367 (564)
T ss_pred Hhhhhhh------------------------------------hhehhhhcc--------ccceeeccCcCcccchhhHH
Confidence 5544322 233455333 23499999999999999999
Q ss_pred HHHHHHHhHH
Q 002338 506 WYELKKKQES 515 (934)
Q Consensus 506 yy~k~KK~~~ 515 (934)
||..+++++.
T Consensus 368 ~~~~~~klk~ 377 (564)
T COG1293 368 YFKKYKKLKG 377 (564)
T ss_pred HhhhhhhccC
Confidence 9999999963
No 6
>KOG3272 consensus Predicted coiled-coil protein [General function prediction only]
Probab=97.51 E-value=0.00031 Score=71.33 Aligned_cols=89 Identities=19% Similarity=0.293 Sum_probs=71.8
Q ss_pred ccCCeEEEecCChhhHHHHHHHhcCCCCEEEEecCCCCcEEEEecCCCCC---CCCHHHHHHHHHHHHHhcccc-CCCCc
Q 002338 565 SSENYLVISGRDAQQNEMIVKRYMSKGDVYVHADLHGASSTVIKNHRPEQ---PVPPLTLNQAGCFTVCHSQAW-DSKMV 640 (934)
Q Consensus 565 SSdGylVivGRDa~QNE~LvkKya~~~Diw~HAdi~GAShVIIKn~~~g~---~ip~~tL~eAA~lAa~ySkAW-~sk~V 640 (934)
+...|.++.|+|-..|+.|. +|.-++|+|||++---++||.|+-. +++ .||...|.++|+|+-.-|--= .-..|
T Consensus 10 t~~~~~i~mg~dk~en~~lI-k~g~~e~Vwfhv~~~sS~hvyl~l~-~~qtiddip~~vL~DC~QLvKaNSIQG~Kmnnv 87 (207)
T KOG3272|consen 10 TEPPYMIYMGKDKFENEELI-KWGWPEDVWFHVDKLSSAHVYLRLR-EGQTIDDIPEFVLEDCAQLVKANSIQGNKMNNV 87 (207)
T ss_pred CCCCeeEEEeecccchhHHH-HcCCccceEEEeecccccceeeeec-CCCCcccccHHHHHHHHHHHHhcccccccccce
Confidence 34489999999999999998 6999999999997777788999875 444 589999999999998887432 22235
Q ss_pred ceEEEEecccccccCC
Q 002338 641 TSAWWVYPHQVSKTAP 656 (934)
Q Consensus 641 ~sa~wV~~~QVSKtap 656 (934)
. +-|+.-+.+.||+-
T Consensus 88 ~-VvYT~w~NLKKt~~ 102 (207)
T KOG3272|consen 88 E-VVYTPWSNLKKTAD 102 (207)
T ss_pred e-EEechhHhhcccCC
Confidence 4 44799999999874
No 7
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=95.99 E-value=0.26 Score=54.59 Aligned_cols=51 Identities=20% Similarity=0.343 Sum_probs=42.9
Q ss_pred hhHHHHH---hhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHH
Q 002338 238 PTLKTVL---GEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKF 291 (934)
Q Consensus 238 ~~lk~~L---~~~~g~gp~laeei~~ragl~~~~~~~~~~~l~~~~~~~L~~al~~~ 291 (934)
..++.+| ..+.|+|..+++|+|++|||.|..++. .|+++++..|+.++..+
T Consensus 156 ~~Ik~~LLDQ~~iaGiGNiya~EiLf~a~I~P~~~~~---~Ls~~~~~~L~~~~~~v 209 (274)
T PRK01103 156 TAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAG---SLSRAEAERLVDAIKAV 209 (274)
T ss_pred ccHHHHhhcCCeEecccHhHHHHHHHHcCCCccCccc---cCCHHHHHHHHHHHHHH
Confidence 4577777 567899999999999999999998764 68999999999886544
No 8
>PRK10445 endonuclease VIII; Provisional
Probab=95.40 E-value=0.23 Score=54.65 Aligned_cols=50 Identities=24% Similarity=0.391 Sum_probs=39.7
Q ss_pred hHHHHH-h--hhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHH
Q 002338 239 TLKTVL-G--EALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKF 291 (934)
Q Consensus 239 ~lk~~L-~--~~~g~gp~laeei~~ragl~~~~~~~~~~~l~~~~~~~L~~al~~~ 291 (934)
.+|.+| . .+.|+|..++.|+|++|||.|..++. .|+++++.+|+.++..+
T Consensus 153 ~IK~~LLDQ~~vaGIGNiyadEiLf~A~I~P~~~~~---~Ls~~~~~~L~~~i~~v 205 (263)
T PRK10445 153 QFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAK---DLNEAQLDALAHALLDI 205 (263)
T ss_pred cHHHHHhcCCccccccHHHHHHHHHHcCCCcCCCcc---cCCHHHHHHHHHHHHHH
Confidence 344444 3 25599999999999999999998764 68999999999886544
No 9
>KOG2030 consensus Predicted RNA-binding protein [General function prediction only]
Probab=94.55 E-value=0.01 Score=71.63 Aligned_cols=97 Identities=22% Similarity=0.207 Sum_probs=70.3
Q ss_pred ccccccccCCcccchHHHHHhhcCCCCCCCCc-hhhhhhhccC-----CCCCCCcccccccccCCCCCCCcccch-----
Q 002338 831 VERTATVRDKPYISKAERRKLKKGQGSSVVDP-KVEREKERGK-----DASSQPESIVRKTKIEGGKISRGQKGK----- 899 (934)
Q Consensus 831 ~~~~~~~~~~~~~s~~~~~~~kk~~~~~~~~~-~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~rg~~~k----- 899 (934)
......++.+.++|+++|+.||.......+.+ ..-..+...+ -.......+.+..+..-..+++|+..|
T Consensus 139 ~~~~~~~rer~~~s~~e~~~~k~~~~le~s~dlk~~~~~~q~g~~~~~il~~~~~~g~sk~k~~v~~~~~~~~sKsse~~ 218 (911)
T KOG2030|consen 139 ESSRSASRERFDFSAKERNEMKSVKKLEKSGDLKALEPKDQNGITLESILHIETKEGPSKIKHIVLDMKKGQLSKSSENI 218 (911)
T ss_pred cchhhhhhhhcchhhhhhhhccccchhhhcchHHHhhccCccccchhhhhhhhccCCCccchhhhhhhcccccccccccc
Confidence 45566789999999999999999887777643 2222211112 111122333334444566789999999
Q ss_pred ------hhhhhhhhcCCChHHHHHHHHHHhccCC
Q 002338 900 ------LKKMKEKYGDQDEEERNIRMALLAVSTL 927 (934)
Q Consensus 900 ------~kk~~~ky~dqdee~r~~~m~~l~~~~~ 927 (934)
+++++++|.||+|+.|+++|.++++.|.
T Consensus 219 ~~~~~~i~~l~e~v~~~eE~~~elit~~~~~~Gy 252 (911)
T KOG2030|consen 219 KLFDSEIKKLQEAVKDQEEEDRELITGKLGSKGY 252 (911)
T ss_pred cccchhhHHHHHHHHHHHHHHHHHHhCCCcccch
Confidence 9999999999999999999999998885
No 10
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=94.50 E-value=0.79 Score=50.67 Aligned_cols=50 Identities=16% Similarity=0.206 Sum_probs=40.0
Q ss_pred hHHHHHh---hhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHH
Q 002338 239 TLKTVLG---EALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKF 291 (934)
Q Consensus 239 ~lk~~L~---~~~g~gp~laeei~~ragl~~~~~~~~~~~l~~~~~~~L~~al~~~ 291 (934)
.++.+|. .+.|+|..++.|+|++|||.|..+.. .|+++++..|+.++..+
T Consensus 145 ~Ik~~LlDQ~~iaGIGNiyadEiLf~A~I~P~~~~~---~Ls~~~~~~L~~~i~~v 197 (269)
T PRK14811 145 PVKPWLLSQKPVAGVGNIYADESLWRARIHPARPAT---SLKAPEARRLYRAIREV 197 (269)
T ss_pred cHHHHHhcCceeecccHHHHHHHHHHcCCCccCCcc---cCCHHHHHHHHHHHHHH
Confidence 4555543 35699999999999999999998764 68999999998885543
No 11
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=94.01 E-value=1.6 Score=48.49 Aligned_cols=50 Identities=20% Similarity=0.361 Sum_probs=40.4
Q ss_pred hHHHHHh---hhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHH
Q 002338 239 TLKTVLG---EALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKF 291 (934)
Q Consensus 239 ~lk~~L~---~~~g~gp~laeei~~ragl~~~~~~~~~~~l~~~~~~~L~~al~~~ 291 (934)
.++.+|. .+.|+|..++.|+|++|||.|..++. .|++++++.|+.++..+
T Consensus 166 ~IK~~LLDQ~~vaGIGNiya~EiLf~A~IhP~~~~~---~Ls~~~~~~L~~~i~~v 218 (282)
T PRK13945 166 SIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAG---QLKKKQLERLREAIIEV 218 (282)
T ss_pred cHHHHhhcCCeEeccchhHHHHHHHHcCCCccCccc---cCCHHHHHHHHHHHHHH
Confidence 4555553 36699999999999999999998764 68999999999886544
No 12
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=93.83 E-value=1.4 Score=48.75 Aligned_cols=50 Identities=20% Similarity=0.359 Sum_probs=40.4
Q ss_pred hHHHHHh---hhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHH
Q 002338 239 TLKTVLG---EALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKF 291 (934)
Q Consensus 239 ~lk~~L~---~~~g~gp~laeei~~ragl~~~~~~~~~~~l~~~~~~~L~~al~~~ 291 (934)
.++.+|. .+.|+|..++.|+|++|||.|..++. .|+++++.+|+.++..+
T Consensus 157 ~Ik~~LlDQ~vvaGIGNiyadEiLf~a~I~P~~~~~---~Ls~~~~~~L~~~i~~v 209 (272)
T TIGR00577 157 KIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLAN---SLSKEECELLHRAIKEV 209 (272)
T ss_pred cHHHHHhcCCeEecccHHHHHHHHHHcCCCcchhhc---cCCHHHHHHHHHHHHHH
Confidence 4555554 35699999999999999999998764 68999999999886544
No 13
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=92.80 E-value=4.3 Score=44.89 Aligned_cols=42 Identities=19% Similarity=0.348 Sum_probs=34.8
Q ss_pred hcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHH
Q 002338 247 ALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKF 291 (934)
Q Consensus 247 ~~g~gp~laeei~~ragl~~~~~~~~~~~l~~~~~~~L~~al~~~ 291 (934)
..|+|..++.|+|+++||.|..+.+ .|+.+++..|++++..+
T Consensus 168 vaGvGNIYa~E~Lf~agI~P~~~a~---~l~~~~~~~l~~~i~~v 209 (273)
T COG0266 168 VAGVGNIYADEILFRAGIHPARPAG---DLSLAQLALLHEAIKDV 209 (273)
T ss_pred eecccHHHHHHHHHHcCCCcccCcc---ccCHHHHHHHHHHHHHH
Confidence 5699999999999999999997764 58888888888775433
No 14
>PF06831 H2TH: Formamidopyrimidine-DNA glycosylase H2TH domain; InterPro: IPR015886 This entry represents a helix-2turn-helix DNA-binding domain found in DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway []. These enzymes are primarily from bacteria, and have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC). Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines [, ]. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above (3.2.2 from EC, 4.2.99.18 from EC), but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine []. These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger []. The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger []. This entry represents the central domain containing the DNA-binding helix-two turn-helix domain [].; GO: 0003684 damaged DNA binding, 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0008270 zinc ion binding, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds, 0006289 nucleotide-excision repair; PDB: 3GQ3_A 3JR5_A 3SAT_A 3GPX_A 2F5Q_A 3SBJ_A 3U6S_A 3SAU_A 3SAR_A 2F5P_A ....
Probab=90.91 E-value=0.52 Score=43.59 Aligned_cols=50 Identities=22% Similarity=0.391 Sum_probs=37.1
Q ss_pred hHHHHHh---hhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHH
Q 002338 239 TLKTVLG---EALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKF 291 (934)
Q Consensus 239 ~lk~~L~---~~~g~gp~laeei~~ragl~~~~~~~~~~~l~~~~~~~L~~al~~~ 291 (934)
.++.+|. .+.|+|..++.|+|+++|+.|..++. .|+++++.+|+.++..+
T Consensus 25 ~ik~~LlDQ~~iaGiGNiy~~EiLf~a~i~P~~~~~---~L~~~~~~~l~~~~~~v 77 (92)
T PF06831_consen 25 PIKAALLDQSVIAGIGNIYADEILFRAGIHPERPAS---SLSEEELRRLHEAIKRV 77 (92)
T ss_dssp BHHHHHHCTTTSTT--HHHHHHHHHHTTB-TTSBGG---GSHHHHHHHHHHHHHHH
T ss_pred hHHHHHhCCCccccCcHHHHHHHHHHcCCCccCccc---cCCHHHHHHHHHHHHHH
Confidence 4555553 36699999999999999999998774 58899999998885543
No 15
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=90.43 E-value=0.56 Score=51.91 Aligned_cols=51 Identities=20% Similarity=0.319 Sum_probs=41.8
Q ss_pred hhHHHHHhh---hcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHH
Q 002338 238 PTLKTVLGE---ALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKF 291 (934)
Q Consensus 238 ~~lk~~L~~---~~g~gp~laeei~~ragl~~~~~~~~~~~l~~~~~~~L~~al~~~ 291 (934)
..++.+|.. +.|+|..+++|+|++|||.|..++. .|+++++..|+.++..+
T Consensus 155 ~~ik~~Lldq~viaGiGNiya~EiLf~a~i~P~~~~~---~l~~~~~~~l~~a~~~v 208 (272)
T PRK14810 155 TRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLAS---SLSRERLRKLHDAIGEV 208 (272)
T ss_pred ccHHHHhhcCceeccccHhHHHHHHHHcCCCCCCCcc---cCCHHHHHHHHHHHHHH
Confidence 356676664 4799999999999999999998764 68999999999885543
No 16
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=86.22 E-value=1.8 Score=41.18 Aligned_cols=49 Identities=24% Similarity=0.365 Sum_probs=40.4
Q ss_pred hhHHHHHhhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHH
Q 002338 238 PTLKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVA 289 (934)
Q Consensus 238 ~~lk~~L~~~~g~gp~laeei~~ragl~~~~~~~~~~~l~~~~~~~L~~al~ 289 (934)
..+...|....|+|+..|..+|..+|++|+.++. .|+++++..|...+.
T Consensus 11 k~i~~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~---~Ls~~~i~~l~~~i~ 59 (107)
T PF00416_consen 11 KPIYIALTKIYGIGRRKAKQICKKLGINPNKKVG---DLSDEQIDKLRKIIE 59 (107)
T ss_dssp SBHHHHHTTSTTBCHHHHHHHHHHTTS-SSSBTT---TSTHHHHHHHHHHHH
T ss_pred cchHhHHhhhhccCHHHHHHHHHHcCCChhhhcc---cCCHHHHHHHHHHHH
Confidence 3577889999999999999999999999998775 589999887665543
No 17
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=85.86 E-value=1.1 Score=43.19 Aligned_cols=47 Identities=21% Similarity=0.341 Sum_probs=39.6
Q ss_pred HHHHHhhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHH
Q 002338 240 LKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVA 289 (934)
Q Consensus 240 lk~~L~~~~g~gp~laeei~~ragl~~~~~~~~~~~l~~~~~~~L~~al~ 289 (934)
+.-+|..+.|+|...+.+||..+|++|+..+. +|+++++.+|-+++.
T Consensus 15 v~iALt~IyGIG~~~a~~I~~~~gi~~~~r~~---eLteeei~~ir~~i~ 61 (121)
T COG0099 15 VVIALTYIYGIGRRRAKEICKKAGIDPDKRVG---ELTEEEIERLRDAIQ 61 (121)
T ss_pred EeehhhhhccccHHHHHHHHHHcCCCHhHhhc---cCCHHHHHHHHHHHH
Confidence 34457788999999999999999999998775 699999988777654
No 18
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=85.09 E-value=0.96 Score=44.14 Aligned_cols=48 Identities=19% Similarity=0.332 Sum_probs=40.2
Q ss_pred hHHHHHhhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHH
Q 002338 239 TLKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVA 289 (934)
Q Consensus 239 ~lk~~L~~~~g~gp~laeei~~ragl~~~~~~~~~~~l~~~~~~~L~~al~ 289 (934)
.+...|..+.|+|+..|..+|..+|++|+.++. .|+++++..|...+.
T Consensus 14 ~v~~aLt~i~GIG~~~A~~ic~~lgi~~~~~~~---~Lt~~qi~~l~~~i~ 61 (122)
T CHL00137 14 RIEYALTYIYGIGLTSAKEILEKANIDPDIRTK---DLTDEQISALREIIE 61 (122)
T ss_pred EeeeeecccccccHHHHHHHHHHcCcCcCcCcc---cCCHHHHHHHHHHHH
Confidence 345567889999999999999999999998875 589999888776653
No 19
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=84.64 E-value=0.84 Score=44.52 Aligned_cols=48 Identities=17% Similarity=0.352 Sum_probs=40.2
Q ss_pred hHHHHHhhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHH
Q 002338 239 TLKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVA 289 (934)
Q Consensus 239 ~lk~~L~~~~g~gp~laeei~~ragl~~~~~~~~~~~l~~~~~~~L~~al~ 289 (934)
.+...|..+.|+|+..|..+|..+|++|+.++. .|+++++..|...|.
T Consensus 14 ~v~~aL~~I~GIG~~~a~~i~~~lgi~~~~~~~---~L~~~qi~~l~~~i~ 61 (122)
T PRK05179 14 RVVIALTYIYGIGRTRAKEILAAAGIDPDTRVK---DLTDEELDKIREEID 61 (122)
T ss_pred EEEeeecccccccHHHHHHHHHHhCcCcccccc---cCCHHHHHHHHHHHH
Confidence 345567889999999999999999999998875 689999888776654
No 20
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=81.70 E-value=1.2 Score=42.77 Aligned_cols=47 Identities=15% Similarity=0.364 Sum_probs=39.6
Q ss_pred hHHHHHhhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHH
Q 002338 239 TLKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAV 288 (934)
Q Consensus 239 ~lk~~L~~~~g~gp~laeei~~ragl~~~~~~~~~~~l~~~~~~~L~~al 288 (934)
.+...|..+.|+|+..|..+|..+|++|+.++. .|+++++..|...|
T Consensus 12 ~v~~aL~~i~GIG~~~a~~i~~~lgi~~~~~~~---~L~~~qi~~l~~~l 58 (113)
T TIGR03631 12 RVEIALTYIYGIGRTRARKILEKAGIDPDKRVK---DLTEEELNAIREEI 58 (113)
T ss_pred EEeeeeeeeecccHHHHHHHHHHhCcCcccccc---cCCHHHHHHHHHHH
Confidence 445567889999999999999999999998875 58999988877665
No 21
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=79.82 E-value=2.3 Score=43.07 Aligned_cols=46 Identities=15% Similarity=0.226 Sum_probs=38.1
Q ss_pred HHHHHhhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHH
Q 002338 240 LKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAV 288 (934)
Q Consensus 240 lk~~L~~~~g~gp~laeei~~ragl~~~~~~~~~~~l~~~~~~~L~~al 288 (934)
+...|..+.|+|+..|..+|.++|++++.+++ +|+++++..|...|
T Consensus 28 v~~aLt~I~GIG~~~A~~I~~~lgi~~~~~~~---~Lt~~qi~~l~~~i 73 (154)
T PTZ00134 28 VPYALTAIKGIGRRFAYLVCKKAGIDVTKRAG---ELTAEEIEKIVEII 73 (154)
T ss_pred EEEeecccccccHHHHHHHHHHcCcCcCCCcc---cCCHHHHHHHHHHH
Confidence 44557788999999999999999999998875 68999987765553
No 22
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=77.64 E-value=2.4 Score=42.79 Aligned_cols=47 Identities=30% Similarity=0.364 Sum_probs=38.8
Q ss_pred hHHHHHhhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHH
Q 002338 239 TLKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAV 288 (934)
Q Consensus 239 ~lk~~L~~~~g~gp~laeei~~ragl~~~~~~~~~~~l~~~~~~~L~~al 288 (934)
.+...|..+.|+|+..|..+|..+|++++.+++ +|+++++..|...|
T Consensus 22 ~i~~aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~---~Lt~~qi~~l~~~i 68 (149)
T PRK04053 22 PVEYALTGIKGIGRRTARAIARKLGLDPNAKLG---YLSDEEIEKIEEAL 68 (149)
T ss_pred EEeeeccccccccHHHHHHHHHHcCcCCCCccC---cCCHHHHHHHHHHH
Confidence 445567889999999999999999999998875 68999987765553
No 23
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=74.91 E-value=4.1 Score=40.93 Aligned_cols=47 Identities=32% Similarity=0.408 Sum_probs=38.7
Q ss_pred HHHHHhhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHH
Q 002338 240 LKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVA 289 (934)
Q Consensus 240 lk~~L~~~~g~gp~laeei~~ragl~~~~~~~~~~~l~~~~~~~L~~al~ 289 (934)
+..+|..+.|+|+..|..+|.++|++++.+++ +|+++++..|...|.
T Consensus 19 v~~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~---~Lt~~qi~~l~~~i~ 65 (144)
T TIGR03629 19 VEYALTGIKGIGRRFARAIARKLGVDPNAKLG---YLDDEEIEKLEEAVE 65 (144)
T ss_pred EEEeecceeccCHHHHHHHHHHcCcCCCCCcc---cCCHHHHHHHHHHHH
Confidence 44557788999999999999999999998875 689999887665543
No 24
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=67.81 E-value=31 Score=41.96 Aligned_cols=51 Identities=33% Similarity=0.406 Sum_probs=42.6
Q ss_pred hhHHHHHh-hhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHH
Q 002338 238 PTLKTVLG-EALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKF 291 (934)
Q Consensus 238 ~~lk~~L~-~~~g~gp~laeei~~ragl~~~~~~~~~~~l~~~~~~~L~~al~~~ 291 (934)
.++..+|. .|..+|+..|+++|..+|+++++++. .|+.+++.+|+++++.+
T Consensus 256 ~~l~~fL~~~f~~v~~~~a~~~~~~~~~~~~~~~~---~l~~~~~~~l~~~~~~~ 307 (535)
T PRK04184 256 RTLKEFLVEEFSRVGDKTADEILEKAGLDPNKKPK---ELTREELERLVEAFKKY 307 (535)
T ss_pred CCHHHHHHHhhcccCHHHHHHHHHHcCCCCCCChh---hCCHHHHHHHHHHHHhc
Confidence 35656665 57799999999999999999988774 58899999999998776
No 25
>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]
Probab=57.47 E-value=2.2e+02 Score=28.82 Aligned_cols=38 Identities=16% Similarity=0.254 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Q 002338 395 RVHTLKQEVDRSVKMAELIEYNLEDVDAAILAVRVALA 432 (934)
Q Consensus 395 ri~~L~~e~e~~~~~aeLI~~Nl~~V~~~i~~v~~a~a 432 (934)
.++.|..+...+....+.|.+.+..+..++.-++.+++
T Consensus 7 ~le~l~a~lq~l~~qie~L~~~i~~l~~~~~e~~~~~~ 44 (145)
T COG1730 7 ELEELAAQLQILQSQIESLQAQIAALNAAISELQTAIE 44 (145)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455555556666666666777777766666666654
No 26
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=49.77 E-value=92 Score=37.55 Aligned_cols=51 Identities=20% Similarity=0.195 Sum_probs=40.3
Q ss_pred hhHHHHHh-hhcCCCHHHHHHHHHHcCCC---CCCcccccccCCHHHHHHHHHHHHHH
Q 002338 238 PTLKTVLG-EALGYGPALSEHIILDTGLV---PNMKLSEVNKLEDNAIQVLVLAVAKF 291 (934)
Q Consensus 238 ~~lk~~L~-~~~g~gp~laeei~~ragl~---~~~~~~~~~~l~~~~~~~L~~al~~~ 291 (934)
.++..+|. .|..+|+..|++++..+|++ +++++. .|+.+++.+|+++++..
T Consensus 247 ~~l~~fL~~~f~~v~~~~a~~~~~~~g~~~~~~~~~~~---~l~~~~~~~l~~~~~~~ 301 (488)
T TIGR01052 247 STLRSFLVSEFSRIGEKKIKELLEKYGIDVDPLDKKPK---ELTWDEAEKIVNAFKEM 301 (488)
T ss_pred ccHHHHHHHhhcccCHHHHHHHHHHhCCCccccCCChh---hCCHHHHHHHHHHHHhc
Confidence 35555554 57799999999999999988 666653 58899999999997753
No 27
>KOG0407 consensus 40S ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=46.73 E-value=62 Score=30.86 Aligned_cols=24 Identities=33% Similarity=0.624 Sum_probs=20.4
Q ss_pred HhcCCCCEEEEe-cCCCCcEEEEecC
Q 002338 586 RYMSKGDVYVHA-DLHGASSTVIKNH 610 (934)
Q Consensus 586 Kya~~~Diw~HA-di~GAShVIIKn~ 610 (934)
=|+..||-|||. |+.| .-+|+|-.
T Consensus 21 i~asfndtfvhitdlsg-~eti~rvt 45 (139)
T KOG0407|consen 21 IFASFNDTFVHVTDLSG-KETIVRVT 45 (139)
T ss_pred EEeecccceEEEeccCC-ceEEEEec
Confidence 378999999999 9999 67888864
No 28
>PF13077 DUF3909: Protein of unknown function (DUF3909)
Probab=44.83 E-value=17 Score=32.85 Aligned_cols=28 Identities=25% Similarity=0.606 Sum_probs=21.6
Q ss_pred HHHHHhcCCC-CEEEEecCCCCcEEEEec
Q 002338 582 MIVKRYMSKG-DVYVHADLHGASSTVIKN 609 (934)
Q Consensus 582 ~LvkKya~~~-Diw~HAdi~GAShVIIKn 609 (934)
+|-.||-|.+ |+|+||++-|-.||-|--
T Consensus 64 ylalkydrdgi~lym~aeidg~~~vsvsy 92 (108)
T PF13077_consen 64 YLALKYDRDGIDLYMHAEIDGVCYVSVSY 92 (108)
T ss_pred HHhheecccceeEEEEeeeccEEEEEEee
Confidence 3556677665 999999999988887654
No 29
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=39.72 E-value=73 Score=37.79 Aligned_cols=53 Identities=23% Similarity=0.308 Sum_probs=40.9
Q ss_pred chhHHHHHh-hhcCCCHHHHHHHHHHcCCCCCCcccccccCC----HHHHHHHHHHHHHHH
Q 002338 237 QPTLKTVLG-EALGYGPALSEHIILDTGLVPNMKLSEVNKLE----DNAIQVLVLAVAKFE 292 (934)
Q Consensus 237 ~~~lk~~L~-~~~g~gp~laeei~~ragl~~~~~~~~~~~l~----~~~~~~L~~al~~~~ 292 (934)
..+++.+|. .|.-+|-..|++++..+|++++.++. .|. .+++++|+++++..+
T Consensus 255 ~~tv~~fL~sef~rig~~ta~e~~e~~g~~~~~~p~---~L~~~~~~eea~~lv~a~~~~~ 312 (538)
T COG1389 255 RSTVREFLVSEFSRIGEKTADELLEYAGFDPDKKPR---ELTKKKTREEAEKLVEAFKKMK 312 (538)
T ss_pred hhhHHHHHHHHHHHhhhhhHHHHHHHhcCCcccCHH---HhhcccCHHHHHHHHHHHHhCc
Confidence 345666654 56689999999999999999987654 355 788888998877654
No 30
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=39.65 E-value=25 Score=44.33 Aligned_cols=9 Identities=22% Similarity=0.243 Sum_probs=5.3
Q ss_pred EeeeccccC
Q 002338 668 IRGKKNFLP 676 (934)
Q Consensus 668 IrGkKnflp 676 (934)
|-|+|+-|.
T Consensus 1356 i~v~R~~~D 1364 (1516)
T KOG1832|consen 1356 IPVDRCLLD 1364 (1516)
T ss_pred eecccchhh
Confidence 566666543
No 31
>PF09602 PhaP_Bmeg: Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg); InterPro: IPR011728 This entry describes a protein found in polyhydroxyalkanoic acid (PHA) gene regions and incorporated into PHA inclusions in Bacillus cereus and Bacillus megaterium. The role of the protein may include amino acid storage [].
Probab=32.40 E-value=5.9e+02 Score=26.40 Aligned_cols=34 Identities=15% Similarity=0.178 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Q 002338 499 AHANARRWYELKKKQESKQEKTITAHSKAFKAAE 532 (934)
Q Consensus 499 a~~NA~~yy~k~KK~~~K~ekt~~a~~~alk~aE 532 (934)
..++...|+++.++.+.-.+|...+.-..++...
T Consensus 123 ~eEtv~~~ieqqk~~r~e~qk~~~~yv~~~k~~q 156 (165)
T PF09602_consen 123 YEETVKQLIEQQKLTREEWQKVLDAYVEQAKSSQ 156 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3466777777776665544555554444444433
No 32
>PF06099 Phenol_hyd_sub: Phenol hydroxylase subunit; InterPro: IPR010353 This family consists of several bacterial phenol hydroxylase subunit proteins, which are part of a multicomponent phenol hydroxylase. Some bacteria can utilise phenol or some of its methylated derivatives as their sole source of carbon and energy. The first step in this process is the conversion of phenol into catechol. Catechol is then further metabolised via the meta-cleavage pathway into TCA cycle intermediates [].
Probab=30.62 E-value=90 Score=26.76 Aligned_cols=31 Identities=29% Similarity=0.413 Sum_probs=25.3
Q ss_pred CceeEEEeeCCCeEEEEEEeeCCceEEEEEEEe
Q 002338 93 RRLEDVRQLGYDRIILFQFGLGMNAHYVILELY 125 (934)
Q Consensus 93 ~RL~~V~Qlg~DRIV~~~f~~G~~~~~LIvEL~ 125 (934)
.|-+.|....-|+.|+|.|+-|+ =.|.|||+
T Consensus 9 ~ryVRv~~~~~~gfVEFeFaIG~--PeL~VELv 39 (59)
T PF06099_consen 9 RRYVRVTGRRDDGFVEFEFAIGD--PELFVELV 39 (59)
T ss_pred cCEEEEecccCCCeEEEEEecCC--cceeEEec
Confidence 34556777789999999999987 47999987
No 33
>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.67 E-value=43 Score=33.90 Aligned_cols=70 Identities=19% Similarity=0.134 Sum_probs=50.9
Q ss_pred eEEEecCChhhHHHHHHHhcCCCCEEEEecCCCCcEEEEec----CCCCCCCCHHHHHHHHHHHHHhccccCCCCc
Q 002338 569 YLVISGRDAQQNEMIVKRYMSKGDVYVHADLHGASSTVIKN----HRPEQPVPPLTLNQAGCFTVCHSQAWDSKMV 640 (934)
Q Consensus 569 ylVivGRDa~QNE~LvkKya~~~Diw~HAdi~GAShVIIKn----~~~g~~ip~~tL~eAA~lAa~ySkAW~sk~V 640 (934)
..|-.|.|+-.+.++ .+++++||.+-+|++=|+.+|=|. ++.|+.-.+.+|.++=.+==..-+.+.+|..
T Consensus 47 v~V~~g~DaaD~~Iv--~~a~~gDlVVT~Di~LA~~ll~kg~~v~~prGr~y~~~nI~~~L~~R~~~~~lR~~G~~ 120 (150)
T COG1671 47 VVVDAGFDAADDWIV--NLAEKGDLVVTADIPLASLLLDKGAAVLNPRGRLYTEENIGERLAMRDFMAKLRRQGKK 120 (150)
T ss_pred EEecCCcchHHHHHH--HhCCCCCEEEECchHHHHHHHhcCCEEECCCCcccCHhHHHHHHHHHHHHHHHHHhccc
Confidence 346678999998877 799999999999999777655442 1257778899998876655555555555543
No 34
>PF04568 IATP: Mitochondrial ATPase inhibitor, IATP; InterPro: IPR007648 ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation [] ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP []. The minimum inhibitory region for bovine inhibitor (P01096 from SWISSPROT) is from residues 39 to 72 []. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH , the inhibitor forms a dimer via antiparallel coiled coil interactions between the C-terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity []. ; GO: 0004857 enzyme inhibitor activity, 0045980 negative regulation of nucleotide metabolic process, 0005739 mitochondrion; PDB: 1GMJ_B 1OHH_H 1HF9_B 2V7Q_J.
Probab=23.85 E-value=3e+02 Score=26.15 Aligned_cols=26 Identities=12% Similarity=0.160 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002338 378 EDAAFHKLNKIHMDQENRVHTLKQEV 403 (934)
Q Consensus 378 e~~~~kkLek~~~~qe~ri~~L~~e~ 403 (934)
.+.++.+|++-+..|++.|+.|++..
T Consensus 74 L~~Lk~kl~~e~~~~~k~i~~le~~I 99 (100)
T PF04568_consen 74 LKKLKEKLKEEIEHHRKEIDELEKHI 99 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34455666666666777777776643
No 35
>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]
Probab=23.48 E-value=1.4e+03 Score=30.79 Aligned_cols=41 Identities=12% Similarity=0.125 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHH-cCCCHHHHHHHH
Q 002338 404 DRSVKMAELIEYNLEDVDAAILAVRVALA-NRMSWEDLARMV 444 (934)
Q Consensus 404 e~~~~~aeLI~~Nl~~V~~~i~~v~~a~a-~g~~W~~i~~~i 444 (934)
++.....+-...+..+++.+|..|+.++. .+.+=+.|+.+-
T Consensus 1457 ~~a~as~~q~~~s~~el~~Li~~v~~Flt~~~adp~si~~vA 1498 (1758)
T KOG0994|consen 1457 EQANASRSQMEESNRELRNLIQQVRDFLTQPDADPDSIEEVA 1498 (1758)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHH
Confidence 33444455566777788889999999884 455666665543
No 36
>PF03993 DUF349: Domain of Unknown Function (DUF349); InterPro: IPR007139 This motif is found singly or as up to five tandem repeats in a small set of bacterial proteins. There are two or three alpha-helices, and possibly a beta-strand.
Probab=22.58 E-value=4.1e+02 Score=22.95 Aligned_cols=14 Identities=36% Similarity=0.681 Sum_probs=11.0
Q ss_pred cHHHHHHHHHHHHH
Q 002338 353 TFDAALDEFYSKIE 366 (934)
Q Consensus 353 sf~~AlDeffs~~e 366 (934)
.|..|+|.||....
T Consensus 6 ~F~~a~~~~~~~~~ 19 (77)
T PF03993_consen 6 RFRAACDAFFDRRK 19 (77)
T ss_pred HHHHHHHHHHHHHH
Confidence 58889999997743
No 37
>PF12925 APP_E2: E2 domain of amyloid precursor protein; InterPro: IPR024329 Amyloid-beta precursor protein (APP, or A4) is associated with Alzheimer's disease (AD), because one of its breakdown products, amyloid-beta (A-beta), aggregates to form amyloid or senile plaques [, ]. Mutations in APP or in proteins that process APP have been linked with early-onset, familial AD. Individuals with Down's syndrome carry an extra copy of chromosome 21, which contains the APP gene, and almost invariably develop amyloid plaques and Alzheimer's symptoms. APP is important for the neurogenesis and neuronal regeneration, either through the intact protein, or through its many breakdown products []. APP consists of a large N-terminal extracellular region containing heparin-binding and copper-binding sites, a short hydrophobic transmembrane domain, and a short C-terminal intracellular domain. The N-terminal region is similar in structure to cysteine-rich growth factors and appears to function as a cell surface receptor, contributing to neurite growth, neuronal adhesion, axonogenesis and cell mobility []. APP acts as a kinesin I membrane receptor to mediate the axonal transport of beta-secretase and presenilin 1. The N-terminal domain can regulate neurite outgrowth through its binding to heparin and collagen I and IV, which are components of the extracellular matrix. APP is also coupled to apoptosis-inducing pathways, and is involved in copper homeostasis/oxidative stress through copper ion reduction, where copper-metallated APP induces neuronal death []. The C-terminal intracellular domain appears to be involved in transcription regulation through protein-protein interactions. APP can promote transcription activation through binding to APBB1/Tip60, and may bind to the adaptor protein FE65 to transactivate a wide variety of different promoters. APP can be processed by different sets of enzymes: In the non-amyloidogenic (non-plaque-forming) pathway, APP is cleaved by alpha-secretase to yield a soluble N-terminal sAPP-alpha (neuroprotective) and a membrane-bound CTF-alpha. CTF-alpha is broken-down by presenilin-containing gamma-secretase to yield soluble p3 and membrane-bound AICD (nuclear signalling). In the amyloidogenic pathway (plaque-forming), APP is broken down by beta-secretase to yield soluble sAPP-beta and membrane-bound CTF-beta. CTF-beta is broken down by gamma-secretase to yield soluble amyloid-beta and membrane-bound AICD. Amyloid-beta is required for neuronal function, but can aggregate to form amyloid plaques that seem to disrupt brain cells by clogging points of cell-cell contact. The E2 domain is the largest of the conserved domains in the amyloidogenic glycoproteins. The structure of E2 consists of two coiled-coil sub-structures connected through a continuous helix, and bears an unexpected resemblance to the spectrin family of protein structures. E2 can reversibly dimerise in solution, and the dimerisation occurs along the longest dimension of the molecule in an antiparallel orientation, which enables the N-terminal substructure of one monomer to pack against the C-terminal substructure of a second monomer. The high degree of conservation of residues at the putative dimer interface suggests that the E2 dimer observed in the crystal could be physiologically relevant. Heparin sulphate proteoglycans, the putative ligands for the precursor present in extracellular matrix, bind to E2 at a conserved and positively charged site near the dimer interface [].; PDB: 3K6B_A 3K66_A 1TKN_A 3NYL_A 3NYJ_A 3UMH_A 3UMK_A 3UMI_A 3QMK_B 3PMR_B ....
Probab=21.46 E-value=8.7e+02 Score=25.85 Aligned_cols=15 Identities=27% Similarity=0.386 Sum_probs=10.3
Q ss_pred HHHHHhHHHHHHHHH
Q 002338 411 ELIEYNLEDVDAAIL 425 (934)
Q Consensus 411 eLI~~Nl~~V~~~i~ 425 (934)
+|...+...|...|.
T Consensus 96 qL~~~H~qRV~a~Ln 110 (193)
T PF12925_consen 96 QLVETHQQRVQAMLN 110 (193)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 777778777765443
No 38
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=21.41 E-value=8e+02 Score=24.28 Aligned_cols=45 Identities=11% Similarity=0.252 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Q 002338 378 EDAAFHKLNKIHMDQENRVHTLKQEVDRSVKMAELIEYNLEDVDA 422 (934)
Q Consensus 378 e~~~~kkLek~~~~qe~ri~~L~~e~e~~~~~aeLI~~Nl~~V~~ 422 (934)
...+...|...++.+..||+.|...+++.....+.|......|..
T Consensus 52 l~~vs~~l~~tKkhLsqRId~vd~klDe~~ei~~~i~~eV~~v~~ 96 (126)
T PF07889_consen 52 LEQVSESLSSTKKHLSQRIDRVDDKLDEQKEISKQIKDEVTEVRE 96 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHh
Confidence 344566677777777788888877777777777776666655554
Done!