Query 001312
Match_columns 1102
No_of_seqs 314 out of 1087
Neff 6.2
Searched_HMMs 46136
Date Thu Mar 28 21:30:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001312.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001312hhsearch_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 3E-185 6E-190 1596.4 57.5 891 2-1094 1-891 (911)
2 COG1293 Predicted RNA-binding 100.0 3E-86 6.4E-91 793.9 49.6 553 2-684 1-564 (564)
3 PF05833 FbpA: Fibronectin-bin 100.0 2.6E-58 5.6E-63 546.5 24.0 409 7-553 1-434 (455)
4 PF11923 DUF3441: Domain of un 100.0 2.7E-30 5.8E-35 247.7 3.4 82 1013-1094 7-96 (112)
5 PF05670 DUF814: Domain of unk 99.9 1.5E-26 3.3E-31 215.3 9.2 90 562-653 1-90 (90)
6 KOG2030 Predicted RNA-binding 98.5 5.5E-09 1.2E-13 125.2 -5.1 80 1017-1096 340-420 (911)
7 KOG3272 Predicted coiled-coil 97.3 0.00065 1.4E-08 70.3 7.9 89 565-656 10-102 (207)
8 COG1293 Predicted RNA-binding 97.3 0.0039 8.5E-08 76.8 15.7 121 347-515 256-377 (564)
9 PRK01103 formamidopyrimidine/5 95.9 0.25 5.4E-06 55.9 16.5 51 238-291 156-209 (274)
10 PRK10445 endonuclease VIII; Pr 95.2 0.29 6.4E-06 54.9 13.7 50 239-291 153-205 (263)
11 PRK14811 formamidopyrimidine-D 94.5 0.74 1.6E-05 51.9 14.7 50 239-291 145-197 (269)
12 PRK13945 formamidopyrimidine-D 94.5 1.3 2.7E-05 50.5 16.6 50 239-291 166-218 (282)
13 TIGR00577 fpg formamidopyrimid 94.4 1.1 2.5E-05 50.5 16.0 50 239-291 157-209 (272)
14 COG0266 Nei Formamidopyrimidin 92.4 4.9 0.00011 45.3 16.5 41 247-290 168-208 (273)
15 PRK14810 formamidopyrimidine-D 88.0 0.87 1.9E-05 51.5 6.0 51 238-291 155-208 (272)
16 PF06831 H2TH: Formamidopyrimi 87.4 0.9 2E-05 42.9 4.8 50 239-291 25-77 (92)
17 PF00416 Ribosomal_S13: Riboso 81.2 3.8 8.2E-05 39.8 6.2 49 238-289 11-59 (107)
18 CHL00137 rps13 ribosomal prote 79.1 2.1 4.6E-05 42.6 3.8 48 239-289 14-61 (122)
19 PRK04184 DNA topoisomerase VI 79.0 1.3E+02 0.0028 37.5 19.6 51 238-291 256-307 (535)
20 COG0099 RpsM Ribosomal protein 78.8 2.9 6.2E-05 41.3 4.4 47 240-289 15-61 (121)
21 PRK05179 rpsM 30S ribosomal pr 78.7 1.8 4E-05 43.1 3.1 48 239-289 14-61 (122)
22 TIGR03631 bact_S13 30S ribosom 75.0 2.6 5.6E-05 41.5 3.0 47 239-288 12-58 (113)
23 PTZ00134 40S ribosomal protein 72.7 4.7 0.0001 41.8 4.3 46 240-288 28-73 (154)
24 PRK04053 rps13p 30S ribosomal 69.1 7.1 0.00015 40.3 4.7 47 239-288 22-68 (149)
25 TIGR03629 arch_S13P archaeal r 66.6 7.9 0.00017 39.8 4.5 47 240-289 19-65 (144)
26 COG1730 GIM5 Predicted prefold 52.4 2.9E+02 0.0062 28.6 13.1 38 395-432 7-44 (145)
27 TIGR01052 top6b DNA topoisomer 51.4 80 0.0017 38.9 10.1 51 238-291 247-301 (488)
28 PF13077 DUF3909: Protein of u 39.7 23 0.00051 32.7 2.4 28 582-609 64-92 (108)
29 KOG0407 40S ribosomal protein 30.8 1.5E+02 0.0032 29.0 6.2 24 586-610 21-45 (139)
30 COG1389 DNA topoisomerase VI, 29.0 1.9E+02 0.0041 35.2 8.1 53 237-292 255-312 (538)
31 COG1671 Uncharacterized protei 27.2 49 0.0011 34.2 2.6 68 570-639 48-119 (150)
32 PF07889 DUF1664: Protein of u 26.9 6.8E+02 0.015 25.4 11.9 49 378-426 52-100 (126)
33 PF06099 Phenol_hyd_sub: Pheno 26.4 1.1E+02 0.0024 26.8 4.2 30 94-125 10-39 (59)
34 PF09602 PhaP_Bmeg: Polyhydrox 24.8 8.5E+02 0.018 25.8 12.0 37 499-535 123-159 (165)
35 KOG1832 HIV-1 Vpr-binding prot 22.9 66 0.0014 41.5 3.1 13 352-364 1013-1025(1516)
36 PRK05264 transcriptional repre 22.0 30 0.00064 32.5 -0.0 16 1020-1035 62-77 (105)
37 cd00490 Met_repressor_MetJ Met 21.5 32 0.0007 32.1 0.1 16 1020-1035 61-76 (103)
38 PF03993 DUF349: Domain of Unk 20.7 5.1E+02 0.011 22.9 7.8 14 352-365 5-18 (77)
39 PF04568 IATP: Mitochondrial A 20.2 3.7E+02 0.0081 26.1 6.9 45 351-403 54-99 (100)
40 PF04048 Sec8_exocyst: Sec8 ex 20.2 6.4E+02 0.014 25.7 9.2 49 350-401 63-111 (142)
No 1
>KOG2030 consensus Predicted RNA-binding protein [General function prediction only]
Probab=100.00 E-value=2.9e-185 Score=1596.44 Aligned_cols=891 Identities=47% Similarity=0.700 Sum_probs=708.1
Q ss_pred ccCCCCHHHHHHHHHHHhhhcCCceeEEEecCCCEEEEEEecCCCCccCCCCceEEEEEeccceEEeccccCCCCCCCCH
Q 001312 2 VKVRMNTADVAAEVKCLRRLIGMRCSNVYDLSPKTYIFKLMNSSGVTESGESEKVLLLMESGVRLHTTAYARDKKNTPSG 81 (1102)
Q Consensus 2 mK~rmsslDv~aiv~EL~~L~G~RI~nIY~~~~~~~llk~~~~~g~~~~g~~~k~~LliesG~RiHlT~~~r~k~~~Ps~ 81 (1102)
|||||++|||.+.|+||+.|.|+||+|||++++++|||||.++ + .|+++||+|||+|.+.|+++.+||+
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 2 7999999999999999999999999
Q ss_pred HHHHHHHHccCCceeEEEeeCCCeEEEEEEeeCCceEEEEEEeccCceEEEEcCCCceEeeecccccCCCccccccCCcc
Q 001312 82 FTLKLRKHIRTRRLEDVRQLGYDRIILFQFGLGMNAHYVILELYAQGNILLTDSEFTVLTLLRSHRDDDKGVAIMSRHRY 161 (1102)
Q Consensus 82 F~m~LRKhL~g~RL~~V~Q~g~DRII~~~F~~G~~~~~LilEL~grgNIILtD~e~~IL~~lR~v~~~~~~~~i~~g~~Y 161 (1102)
|||+|||||+..||++|+|+|+||||+|+||.|+..+|||||||++|||||||.+++||.+||.++.+....+.+++++|
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 99999999999999999999999999999999999999999999999999999999999999999987777888999999
Q ss_pred cCccccccccCChhhHHHhhccCCCCCCCCCCCccCCCCCcccccccccCCCCCCCccccccccCCCCCCCccCCchhHH
Q 001312 162 PTEICRVFERTTASKLHAALTSSKEPDANEPDKVNEDGNNVSNASKENLGGQKGGKSFDLSKNSNKNSNDGARAKQPTLK 241 (1102)
Q Consensus 162 p~~~~~~~~p~~~~~l~~~l~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~lk 241 (1102)
++..+..+..-+.+.+.... +.. +|. .+...+.++.
T Consensus 150 ~~s~~e~~~~k~~~~le~s~----------------dlk-------------------~~~---------~~~q~g~~~~ 185 (911)
T KOG2030|consen 150 DFSAKERNEMKSVKKLEKSG----------------DLK-------------------ALE---------PKDQNGITLE 185 (911)
T ss_pred chhhhhhhhccccchhhhcc----------------hHH-------------------Hhh---------ccCccccchh
Confidence 88765544332222221100 000 000 1112346788
Q ss_pred HHHhhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHHHHHHHHhhcCCCcceEEEEecccCCCCCCC
Q 001312 242 TVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKFEDWLQDVISGDIVPEGYILMQNKHLGKDHP 321 (1102)
Q Consensus 242 ~~L~~~~g~gp~laeei~~~agi~~~~~~~~~~~l~~~~~~~L~~al~~~~~~~~~l~~~~~~p~gyi~~~~~~~~~~~~ 321 (1102)
++|...+++||...+|++..++..+..+.+....+++.++..|.++++.++.|+.++.++...|.|||.+.....+.
T Consensus 186 ~il~~~~~~g~sk~k~~v~~~~~~~~sKsse~~~~~~~~i~~l~e~v~~~eE~~~elit~~~~~~Gyi~~~k~~~~~--- 262 (911)
T KOG2030|consen 186 SILHIETKEGPSKIKHIVLDMKKGQLSKSSENIKLFDSEIKKLQEAVKDQEEEDRELITGKLGSKGYILEEKEKKPI--- 262 (911)
T ss_pred hhhhhhccCCCccchhhhhhhcccccccccccccccchhhHHHHHHHHHHHHHHHHHHhCCCcccchhHHhhcccCC---
Confidence 99999999999999999999998887775555567788999999999999999999999988899999766543221
Q ss_pred CCCCCCCCccceeeeeccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001312 322 PTESGSSTQIYDEFCPLLLNQFRSREFVKFETFDAALDEFYSKIESQRAEQQHKAKEDAAFHKLNKIHMDQENRVHTLKQ 401 (1102)
Q Consensus 322 ~~~~~~~~~~y~~F~Pf~l~q~~~~~~~~f~sfn~avDeffs~~e~qk~~~~~~~~e~~~~kKLek~~~~qe~ri~~L~~ 401 (1102)
+.....|.+||| .+.||...++..|++|++|+|+|||.+++|+.+++....+..+.+||++++++|+++++.|++
T Consensus 263 ----s~~~~~y~~f~p-~~~~fKs~~~k~fetf~ea~Def~S~IEsqk~~lr~~~~E~qa~kKld~vr~Dq~~rvq~Lqq 337 (911)
T KOG2030|consen 263 ----STKEFIYDEFHP-LGVQFKSEPVKKFETFNEAVDEFFSTIESQKSELRVKNQELQAEKKLDKVRKDQKERVQELQQ 337 (911)
T ss_pred ----Cccceeeccccc-cccccccchhhhccchhhHHHHHHHHHhhhhHHHHHHhhHhHHHhhhhcchhhHHHHHHHHHH
Confidence 122578999999 778999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCcccccccccccCceEEEEccCCCCCCcc
Q 001312 402 EVDRSVKMAELIEYNLEDVDAAILAVRVALANRMSWEDLARMVKEERKAGNPVAGLIDKLYLERNCMSLLLSNNLDEMDD 481 (1102)
Q Consensus 402 ~~e~~~~kaeLI~aN~~~V~~ai~~v~~~~a~g~~W~~i~~li~~~~~~gnpvA~~I~~l~l~~n~itl~L~d~~d~~~~ 481 (1102)
.++.++++|+||+.|..+|+.+|.+|++++++||+|.+|.+|++.+|++|||||..|.+++|+.|++|+.|.|+|+|+||
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 99999999999999999999999999999999999999999999999999999999999999999999999999997777
Q ss_pred cccCCCcEEEEeCCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhchhhHHhhhhcccccCce
Q 001312 482 EEKTLPVEKVEVDLALSAHANARRWYELKKKQESKQEKTITAHSKAFKAAEKKTRLQILQEKTVANISHMRKVHWFEKFN 561 (1102)
Q Consensus 482 ~~~~~~~~~I~LDl~lS~~~NA~~YY~k~Kka~~K~ekt~~a~~kalk~aEkk~~~~L~~~~~~~~l~~iRk~~wfEKF~ 561 (1102)
+..+.+.+.|+||++||+|+||++||.++|+++.|+++|..++++||++++.|++++|++.+++..|..+|++|||||||
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 76777788999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecCCceEEecCCchhhHHHHHhhcCCCcEEEEecCCCCcEEEEeCCCCCCCCCHHHHHHHHHHHhHhcccccCCCcc
Q 001312 562 WFISSENYLVISGRDAQQNEMIVKRYMSKGDVYVHADLHGASSTVIKNHRPEQPVPPLTLNQAGCFTVCHSQAWDSKMVT 641 (1102)
Q Consensus 562 wFiSSdGylVi~GRda~QNE~Lv~ky~~~~Diw~HAdi~GAshVIIK~~~~~~~ip~~tL~eAA~lAa~ySkAw~s~~v~ 641 (1102)
|||||+|||||+||||||||+||+|||+|+|||||||+||||||||||+ ++.+|||.||.|||+||+|||+||++++|+
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 899999999999999999999999999999
Q ss_pred eeEEEeceeccccCCCCeeeccCcEEEeeccccCCCCCceeEEEEEEEecccccccccccccccCccCCCCCCCCCCCCC
Q 001312 642 SAWWVYPHQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLIMGFGLLFRLDESSLGSHLNERRVRGEEEGMDDFEDSGHHK 721 (1102)
Q Consensus 642 ~a~wV~~~QVsK~apsGeyL~~GsFmIrGkkn~lpp~~L~mg~g~~f~~~~~~~~~h~~~r~~~~~~~~~~~~~~~~~~~ 721 (1102)
++|||+++|||||||||||||+||||||||||||||++|+|||||||+||++++++|.++|+++.+++...+.+
T Consensus 577 saWwv~~dqVSKtaptgeyL~~GSFmIrgkkN~lpp~~LvmG~GlLfrldes~~E~~~~~r~~~~eee~~~~~e------ 650 (911)
T KOG2030|consen 577 SAWWVYPDQVSKTAPTGEYLPTGSFMIRGKKNFLPPHQLVMGLGLLFRLDESSIERHLGERKVEEEEEKEEDEE------ 650 (911)
T ss_pred cceEEecccccccCCCCccccccceEEecccCCCCchhheecceeEEEeccchhhhhhhhHHHHHHHhhhcccc------
Confidence 99999999999999999999999999999999999999999999999999999999999999886655442210
Q ss_pred CCCcccccCCCCCCccccccCCCCCCCCCCCCCCCCCCCCCCCCCccccccCCCCCcchhhcccccCCCCCcchhhhhhh
Q 001312 722 ENSDIESEKDDTDEKPVAESLSVPNSAHPAPSHTNASNVDSHEFPAEDKTISNGIDSKIFDIARNVAAPVTPQLEDLIDR 801 (1102)
Q Consensus 722 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 801 (1102)
. +..++..+ .++..+.+....+++| ...++..
T Consensus 651 --------~---e~~ee~~s---------~~~e~~~~~~s~~e~~--~~ev~~~-------------------------- 682 (911)
T KOG2030|consen 651 --------P---ELMEEVES---------KTSEIPEEVISNDEFP--VNEVKGR-------------------------- 682 (911)
T ss_pred --------h---hhhhhccc---------ccccCCcccccccccc--ccccccc--------------------------
Confidence 0 00000000 0000000000001111 0000000
Q ss_pred hccCCccCCCCCcccccccccCccccccccccccccCCCCCCchHHHHhhhcCCCCCCCCchhhhhhhhcCCCCCCCccc
Q 001312 802 ALGLGSASISSTKHGIETTQFDLSEEDKHVERTATVRDKPYISKAERRKLKKGQGSSVVDPKVEREKERGKDASSQPESI 881 (1102)
Q Consensus 802 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 881 (1102)
...|+ .. ....++.+....++..++.+..+...+....++..-.....++-..
T Consensus 683 -------~~~Gk---------~~-----------~~~~~~~~~~~~~~~~~k~~s~~~~~~n~~~~k~~~~e~~~~~is~ 735 (911)
T KOG2030|consen 683 -------EKTGK---------NV-----------QEESKTFIGKGPKREKKKVQSASKEEDNVGRAKQRIGESSVQPISD 735 (911)
T ss_pred -------ccCCc---------ch-----------hhhhhhhhhcCccchhhhccccccchhhhhHHHHhhhhcccccccc
Confidence 00000 00 0011222222222322332222111111111000000011111111
Q ss_pred ccccccCCCCCcccchhhhhHHhhhhcCCCHHHHHHHHHHhhccCCCCCCCCCCCCcccccccCCCCCCCCCCcchhhhh
Q 001312 882 VRKTKIEGGKISRGQKGKLKKMKEKYGDQDEEERNIRMALLASAGKVQKNDGDPQNENASTHKEKKPAISPVDAPKVCYK 961 (1102)
Q Consensus 882 ~~~~~~~~~~~~RG~k~K~KKi~~KY~dQDEEdR~l~m~lLgs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 961 (1102)
.+.+ ..+.+||||||+|||+ |+||||+||+|+|+||++.|+ .+...++++... +.+.+.+. ..++
T Consensus 736 ep~~---~~~~~rg~kgklkkmk--y~dQd~~er~~r~~~l~~~~k-ek~~v~~~ev~~-------~~~~~~~~-~k~~- 800 (911)
T KOG2030|consen 736 EPSN---KNQVKRGQKGKLKKMK--YADQDEDERELRMELLKSSGK-EKQQVEEKEVMK-------PEESEDEE-NKRE- 800 (911)
T ss_pred CCcc---hHHHHHhhhhhhhhhh--hcccCchHHHHHHHhcccccc-cccccccccccC-------chhhchhh-cchh-
Confidence 1111 1244899999999998 999999999999999999887 222222111000 00000000 0000
Q ss_pred hhhcCCCCccCCCCCCCCCCCCCCCCCCCCcchhHHhHhhhhhhhhcccchhhhccccccccccCCCCCCCeEEeecccc
Q 001312 962 CKKAGHLSKDCKEHPDDSSHGVEDNPCVGLDETAEMDKVAMEEEDIHEIGEEEKGRLNDVDYLTGNPLPSDILLYVIPVC 1041 (1102)
Q Consensus 962 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ee~~~~~~~e~~~~~~~ld~Ltg~P~~~D~ll~aiPVc 1041 (1102)
...+.| ..+.+.+.+..+. ...|+-|+. ++|+||||||||
T Consensus 801 k~~~~~------------------------------~~ve~~~~d~~~~-------~ee~~~~~d---~~D~ll~avPv~ 840 (911)
T KOG2030|consen 801 KLEAPK------------------------------FKVEEKERDEYEV-------KEELKPLID---KGDTLLFAVPVV 840 (911)
T ss_pred hhhccc------------------------------ccccchhhhccch-------hhhcccccC---CCceeEEeeccc
Confidence 000000 0111111111111 222333333 999999999999
Q ss_pred chhhhhccCeeeEEeccCCccchhHHHHHHHHHHhhccCCccccchhcccccc
Q 001312 1042 GPYSAVQSYKYRVKIIPGTAKKGKGIQIFYSLLLLMLSLTPVFDIFPFQCLCS 1094 (1102)
Q Consensus 1042 APy~al~~yKyKvKl~PG~~KKGKA~k~al~~f~~~~~~~~~~~~l~~~~~~~ 1094 (1102)
|||+||++||||||+|||++|||||||+||++|++.+ ++||++||++|++.
T Consensus 841 aPy~Al~~ykykVKi~PGsgK~gKaak~al~~F~~~~--s~re~~lik~lk~~ 891 (911)
T KOG2030|consen 841 APYNALQKYKYKVKITPGSGKKGKAAKEALNLFTKRP--SPREKELIKSLKDD 891 (911)
T ss_pred cChHHHHhhceeEEecCCcCcccHHHHHHHHHHhcCC--ChhHHHHHHhcchh
Confidence 9999999999999999999999999999999999998 99999999999953
No 2
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=100.00 E-value=3e-86 Score=793.92 Aligned_cols=553 Identities=29% Similarity=0.418 Sum_probs=412.0
Q ss_pred ccCCCCHHHHHHHHHHHh-hhcCCceeEEEecCCCEEEEEEecCCCCccCCCCceEEEEEeccce--EEeccccCCCCCC
Q 001312 2 VKVRMNTADVAAEVKCLR-RLIGMRCSNVYDLSPKTYIFKLMNSSGVTESGESEKVLLLMESGVR--LHTTAYARDKKNT 78 (1102)
Q Consensus 2 mK~rmsslDv~aiv~EL~-~L~G~RI~nIY~~~~~~~llk~~~~~g~~~~g~~~k~~LliesG~R--iHlT~~~r~k~~~ 78 (1102)
||++||++||++++.||+ .|.|+||.||||+..+++.|.|+.++ . .+..|+++.|.| ||+|.+.+..|..
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 69999999999999999999999874 2 467788888866 9999999999999
Q ss_pred CCHHHHHHHHHccCCceeEEEeeCCCeEEEEEEe---eCC-ceEEEEEEeccC-ceEEEEcCCCceEeeecccccCCCcc
Q 001312 79 PSGFTLKLRKHIRTRRLEDVRQLGYDRIILFQFG---LGM-NAHYVILELYAQ-GNILLTDSEFTVLTLLRSHRDDDKGV 153 (1102)
Q Consensus 79 Ps~F~m~LRKhL~g~RL~~V~Q~g~DRII~~~F~---~G~-~~~~LilEL~gr-gNIILtD~e~~IL~~lR~v~~~~~~~ 153 (1102)
||+|||.|||||+|++|++|+|+|+||||+|+|+ .|+ ..++|++|+||+ |||||||++++||+++|++++. .|
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 233 278888888988 9999999999999999999987 46
Q ss_pred ccccCCcccCccccccccCChhh--HHHhhccCCCCCCCCCCCccCCCCCcccccccccCCCCCCCccccccccCCCCCC
Q 001312 154 AIMSRHRYPTEICRVFERTTASK--LHAALTSSKEPDANEPDKVNEDGNNVSNASKENLGGQKGGKSFDLSKNSNKNSND 231 (1102)
Q Consensus 154 ~i~~g~~Yp~~~~~~~~p~~~~~--l~~~l~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~ 231 (1102)
.|.+|..|.+|+...-+|.+... +....
T Consensus 152 ~i~pG~~Y~~Pp~~~~~p~~~~~~~~~~~~-------------------------------------------------- 181 (564)
T COG1293 152 TIKPGEIYILPPAQLKNPYEQSEEDFKELQ-------------------------------------------------- 181 (564)
T ss_pred eecCCCcccCCcccCCChhhcChHHHHHHH--------------------------------------------------
Confidence 89999999877654323433221 11111
Q ss_pred CccCCchhHHHHHhhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHHHHHHHHhhcCCCcceEEEEe
Q 001312 232 GARAKQPTLKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKFEDWLQDVISGDIVPEGYILM 311 (1102)
Q Consensus 232 ~~~~~~~~lk~~L~~~~g~gp~laeei~~~agi~~~~~~~~~~~l~~~~~~~L~~al~~~~~~~~~l~~~~~~p~gyi~~ 311 (1102)
...+..+++++..++|+||.++++++.|+|++++.++. ++..+.+..+..+ +.+|+..+ ..+..|+
T Consensus 182 --~~~~~~~~~~~~~~~g~~~~~a~el~~rag~~~~~~~~---~~~~~~~~~v~~~---~~~~~~~~----~~~~~~~-- 247 (564)
T COG1293 182 --LNSGADIVRLLARFLGLGGLLAEELLSRAGLDKKVPAK---DLFEEEIKKVREA---LEELLNPL----KPNYYYK-- 247 (564)
T ss_pred --hccchHHHHHHHHhcCCCHHHHHHHHHhcCCCcCCchh---hhhHHHHHHHHHH---HHhhhhcc----ccCceee--
Confidence 01255788999999999999999999999999987644 3556677666555 34444433 1122232
Q ss_pred cccCCCCCCCCCCCCCCCccceeeeeccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001312 312 QNKHLGKDHPPTESGSSTQIYDEFCPLLLNQFRSREFVKFETFDAALDEFYSKIESQRAEQQHKAKEDAAFHKLNKIHMD 391 (1102)
Q Consensus 312 ~~~~~~~~~~~~~~~~~~~~y~~F~Pf~l~q~~~~~~~~f~sfn~avDeffs~~e~qk~~~~~~~~e~~~~kKLek~~~~ 391 (1102)
. ..+.+..| +..|.+.. .+||+++|+||.....................+|++....
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 2799999999998654433334555556667788888889
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCcccccccccccCceEEEE
Q 001312 392 QENRVHTLKQEVDRSVKMAELIEYNLEDVDAAILAVRVALANRMSWEDLARMVKEERKAGNPVAGLIDKLYLERNCMSLL 471 (1102)
Q Consensus 392 qe~ri~~L~~~~e~~~~kaeLI~aN~~~V~~ai~~v~~~~a~g~~W~~i~~li~~~~~~gnpvA~~I~~l~l~~n~itl~ 471 (1102)
|++.++.++..++.++++|+||++|++.|+..+..|+.+...+ |..|.. .......|+. +.... ..+...
T Consensus 305 ~~~~~~~~~~~~~~~r~~g~ll~an~~~i~~~~~~v~~~~~~~--~~~i~i---~l~~~~~~~~--~~~~~---~~~~~k 374 (564)
T COG1293 305 QEDELEELEKAAEELRQKGELLYANLQLIEEGLKSVRLADFYG--NEEIKI---ELDKSKTPSE--NAQRY---FKKYKK 374 (564)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhehhhhcc--ccceee---ccCcCcccch--hhHHH---hhhhhh
Confidence 9999999999999999999999999999996666665543332 111100 0000000000 00000 000000
Q ss_pred ccCCCCCCcccccCCCcEEEEeCCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhchhhHHhh
Q 001312 472 LSNNLDEMDDEEKTLPVEKVEVDLALSAHANARRWYELKKKQESKQEKTITAHSKAFKAAEKKTRLQILQEKTVANISHM 551 (1102)
Q Consensus 472 L~d~~d~~~~~~~~~~~~~I~LDl~lS~~~NA~~YY~k~Kka~~K~ekt~~a~~kalk~aEkk~~~~L~~~~~~~~l~~i 551 (1102)
| ....+.|++.++..+|+..||.+.+++.+|... ..+++.+. ++.+++.+.+ ......
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 113455666666666666666666666555544 22222221 1222222221 223445
Q ss_pred hhcccccCceEEEecCCceEEecCCchhhHHHHHhhcCCCcEEEEecCCCCcEEEEeCCCCCCCCCHHHHHHHHHHHhHh
Q 001312 552 RKVHWFEKFNWFISSENYLVISGRDAQQNEMIVKRYMSKGDVYVHADLHGASSTVIKNHRPEQPVPPLTLNQAGCFTVCH 631 (1102)
Q Consensus 552 Rk~~wfEKF~wFiSSdGylVi~GRda~QNE~Lv~ky~~~~Diw~HAdi~GAshVIIK~~~~~~~ip~~tL~eAA~lAa~y 631 (1102)
|++.||++|+||+||+||+||+||||.|||+||+||++++||||||+.+||||||||+ ++..+|+.||.+||.|||||
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-eeEEEeceeccccCCCCeeeccCcEEEeeccccCCCCCceeEE
Q 001312 632 SQAWDSKMVT-SAWWVYPHQVSKTAPTGEYLTVGSFMIRGKKNFLPPHPLIMGF 684 (1102)
Q Consensus 632 SkAw~s~~v~-~a~wV~~~QVsK~apsGeyL~~GsFmIrGkkn~lpp~~L~mg~ 684 (1102)
|+||.++.|+ ++|||++.||+|+|+||+||++|+|||||++||+...+|.+++
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 9999999765 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=2.6e-58 Score=546.46 Aligned_cols=409 Identities=28% Similarity=0.449 Sum_probs=176.7
Q ss_pred CHHHHHHHHHHHh-hhcCCceeEEEecCCCEEEEEEecCCCCccCCCCceEEEEEec---cceEEeccccCCCCCCCCHH
Q 001312 7 NTADVAAEVKCLR-RLIGMRCSNVYDLSPKTYIFKLMNSSGVTESGESEKVLLLMES---GVRLHTTAYARDKKNTPSGF 82 (1102)
Q Consensus 7 sslDv~aiv~EL~-~L~G~RI~nIY~~~~~~~llk~~~~~g~~~~g~~~k~~Llies---G~RiHlT~~~r~k~~~Ps~F 82 (1102)
|++||+|+|.||+ .|+|+||.||||+++++|+|+|++++ ++.+|+|+. |+|||+|.+.+++|..|++|
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 69999999999999999999999763 466788886 89999999999899999999
Q ss_pred HHHHHHHccCCceeEEEeeCCCeEEEEEEeeC-----CceEEEEEEeccC-ceEEEEcCCCceEeeecccccCC-Ccccc
Q 001312 83 TLKLRKHIRTRRLEDVRQLGYDRIILFQFGLG-----MNAHYVILELYAQ-GNILLTDSEFTVLTLLRSHRDDD-KGVAI 155 (1102)
Q Consensus 83 ~m~LRKhL~g~RL~~V~Q~g~DRII~~~F~~G-----~~~~~LilEL~gr-gNIILtD~e~~IL~~lR~v~~~~-~~~~i 155 (1102)
||.|||||+|+||++|+|+|+||||.|+|+.+ ...|+|||||||+ |||||||++++||+++|+++... +.|.|
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 99999999999999999999999999999977 3489999999999 99999999999999999999863 34789
Q ss_pred ccCCcccCcccc-ccccCChhh---HHHhhccCCCCCCCCCCCccCCCCCcccccccccCCCCCCCccccccccCCCCCC
Q 001312 156 MSRHRYPTEICR-VFERTTASK---LHAALTSSKEPDANEPDKVNEDGNNVSNASKENLGGQKGGKSFDLSKNSNKNSND 231 (1102)
Q Consensus 156 ~~g~~Yp~~~~~-~~~p~~~~~---l~~~l~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~ 231 (1102)
.+|.+|.+|+.. ...|.+.+. +...|.
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 999999777652 234544433 222221
Q ss_pred CccCCchhHHHHHhh-hcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHHHHHHHHhhcCCCcceEEEE
Q 001312 232 GARAKQPTLKTVLGE-ALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKFEDWLQDVISGDIVPEGYIL 310 (1102)
Q Consensus 232 ~~~~~~~~lk~~L~~-~~g~gp~laeei~~~agi~~~~~~~~~~~l~~~~~~~L~~al~~~~~~~~~l~~~~~~p~gyi~ 310 (1102)
....++.++|.. +.||||.+++|++.++|+++++++. .++++++..|+.+ +..|+..+.++.+.|.+|
T Consensus 184 ---~~~~~l~~~L~~~~~G~~~~la~ei~~ra~i~~~~~~~---~~~~~~~~~l~~~---~~~l~~~l~~~~~~p~l~-- 252 (455)
T PF05833_consen 184 ---KKEKTLVKALSKNFQGFGPELAEEILYRAGIDKNKKVE---ELSDEEIEKLFEA---IRELLNELEEGQFKPYLY-- 252 (455)
T ss_dssp ---CCG-BHHHHHHHHCTT--HHHHHHHHCCCTS-TTSBGG---G--HHHHCHHHHH---HHHHHHHHT---S----E--
T ss_pred ---cCcccHHHHHHHHHHHhHHHHHHHHHHHhCCCCccccc---cchhhhHHHHHHH---HHHhhhhcccccCccEEE--
Confidence 023455555555 5599999999999999999998876 4778889888877 677888888777666444
Q ss_pred ecccCCCCCCCCCCCCCCCccceeeeeccccccccccccccccHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH
Q 001312 311 MQNKHLGKDHPPTESGSSTQIYDEFCPLLLNQFRSREFVKFETFDAALDEFYSKIES-QRAEQQHKAKEDAAFHKLNKIH 389 (1102)
Q Consensus 311 ~~~~~~~~~~~~~~~~~~~~~y~~F~Pf~l~q~~~~~~~~f~sfn~avDeffs~~e~-qk~~~~~~~~e~~~~kKLek~~ 389 (1102)
+++ ..+..|+||++.++.+.....|+||++|||+||+..+. .++.+ ..+.+.+++++.+
T Consensus 253 ~~~----------------~~~~~f~~~~l~~~~~~~~~~f~s~~~ald~yf~~~~~~~~~~~----~~~~l~k~l~~~~ 312 (455)
T PF05833_consen 253 YDD----------------GKPKDFSPFPLKQYEELEVKEFDSFNEALDEYFSEKEEEERLEQ----KKKRLEKKLEKKI 312 (455)
T ss_dssp EE---------------------EEESS--TT---S--EE-SSHHHHHHHHT----------------------------
T ss_pred Eec----------------CcccEEEEEeccccccccccCCCCHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHH
Confidence 343 24579999999888777788999999999999998653 33333 3344555566666
Q ss_pred HHHHHHHHHHHH------HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCcccccccccc
Q 001312 390 MDQENRVHTLKQ------EVDRSVKMAELIEYNLEDVDAAILAVRVALANRMSWEDLARMVKEERKAGNPVAGLIDKLYL 463 (1102)
Q Consensus 390 ~~qe~ri~~L~~------~~e~~~~kaeLI~aN~~~V~~ai~~v~~~~a~g~~W~~i~~li~~~~~~gnpvA~~I~~l~l 463 (1102)
.+++++++.|++ ..+.++.+|+||++|+|.+. +|++|.++.
T Consensus 313 ~klek~l~~l~~~~~~~~~~~~~~~~gelL~a~~~~i~-----------~g~~~~~l~---------------------- 359 (455)
T PF05833_consen 313 KKLEKKLEKLEEELEESEKAENYREYGELLLANLHQIK-----------KGMKWVELE---------------------- 359 (455)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhh-----------CCCCEEEhh----------------------
Confidence 666677666654 34677889999999999998 999986653
Q ss_pred cCceEEEEccCCCCCCcccccCCCcEEEEeCCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH--HHHHHHHh
Q 001312 464 ERNCMSLLLSNNLDEMDDEEKTLPVEKVEVDLALSAHANARRWYELKKKQESKQEKTITAHSKAFKAAEK--KTRLQILQ 541 (1102)
Q Consensus 464 ~~n~itl~L~d~~d~~~~~~~~~~~~~I~LDl~lS~~~NA~~YY~k~Kka~~K~ekt~~a~~kalk~aEk--k~~~~L~~ 541 (1102)
|++.+ ...++|+|||.+||++||++||++|||+++|.+++..+++.+.+.++. .....++.
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 134899999999999999999999999988877777665554443332 12334555
Q ss_pred hhchhhHHhhhh
Q 001312 542 EKTVANISHMRK 553 (1102)
Q Consensus 542 ~~~~~~l~~iRk 553 (1102)
+.+..+|..+|.
T Consensus 423 a~~~~~l~~i~~ 434 (455)
T PF05833_consen 423 AEDLEELEEIRE 434 (455)
T ss_dssp ------------
T ss_pred cCCHHHHHHHHH
Confidence 556666776664
No 4
>PF11923 DUF3441: Domain of unknown function (DUF3441); InterPro: IPR021846 This presumed domain is functionally uncharacterised. This domain is found in archaea and eukaryotes. This domain is typically between 104 to 119 amino acids in length. This domain is found associated with PF05833 from PFAM, PF05670 from PFAM. This domain has two conserved residues (P and G) that may be functionally important.
Probab=99.96 E-value=2.7e-30 Score=247.75 Aligned_cols=82 Identities=39% Similarity=0.632 Sum_probs=77.0
Q ss_pred hhhccccccccccCCCCCCCeEEeeccccchhhhhccCeeeEEeccCCccchhHHHHHHHHH--------HhhccCCccc
Q 001312 1013 EEKGRLNDVDYLTGNPLPSDILLYVIPVCGPYSAVQSYKYRVKIIPGTAKKGKGIQIFYSLL--------LLMLSLTPVF 1084 (1102)
Q Consensus 1013 e~~~~~~~ld~Ltg~P~~~D~ll~aiPVcAPy~al~~yKyKvKl~PG~~KKGKA~k~al~~f--------~~~~~~~~~~ 1084 (1102)
++.+++..||+|||+|.++|+|+|||||||||+||++||||||||||++|||||||+||++| +++++.++||
T Consensus 7 ~~~e~~~~l~~ltg~P~~~D~il~aVPVcAP~sal~~yKYkvKl~PG~~KKGKaak~il~~f~~~~~d~~~~~~~~~~~e 86 (112)
T PF11923_consen 7 DEAEYLSELDSLTGTPLPEDEILYAVPVCAPYSALSKYKYKVKLQPGNAKKGKAAKEILEYFTARKVDESMKDKDDWPRE 86 (112)
T ss_pred HHHHHHHHHHHhcCCCCCCCEEEEEEEeecCHHHHhhCceeEEEcCCCcchHHHHHHHHHHHHhcccchhhcCccCCHHH
Confidence 34567889999999999999999999999999999999999999999999999999999999 8888899999
Q ss_pred cchhcccccc
Q 001312 1085 DIFPFQCLCS 1094 (1102)
Q Consensus 1085 ~~l~~~~~~~ 1094 (1102)
++|||++++.
T Consensus 87 ~~lik~~~~~ 96 (112)
T PF11923_consen 87 RELIKSIKDN 96 (112)
T ss_pred HHHHccCCHH
Confidence 9999999863
No 5
>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=99.93 E-value=1.5e-26 Score=215.34 Aligned_cols=90 Identities=32% Similarity=0.581 Sum_probs=81.3
Q ss_pred EEEecCCceEEecCCchhhHHHHHhhcCCCcEEEEecCCCCcEEEEeCCCCCCCCCHHHHHHHHHHHhHhcccccCCCcc
Q 001312 562 WFISSENYLVISGRDAQQNEMIVKRYMSKGDVYVHADLHGASSTVIKNHRPEQPVPPLTLNQAGCFTVCHSQAWDSKMVT 641 (1102)
Q Consensus 562 wFiSSdGylVi~GRda~QNE~Lv~ky~~~~Diw~HAdi~GAshVIIK~~~~~~~ip~~tL~eAA~lAa~ySkAw~s~~v~ 641 (1102)
||+||+||+||+|||++|||.|++||++++||||||+.+||||||||++ ..+.++.+|.+||+||||||+||..+...
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 9999999999999999999999999999999999997777799999995 33334449999999999999999888877
Q ss_pred eeEEEeceeccc
Q 001312 642 SAWWVYPHQVSK 653 (1102)
Q Consensus 642 ~a~wV~~~QVsK 653 (1102)
.+||+..++|+|
T Consensus 79 ~V~yt~~k~v~K 90 (90)
T PF05670_consen 79 EVDYTQGKYVKK 90 (90)
T ss_pred EEEEeehHhccC
Confidence 899999999987
No 6
>KOG2030 consensus Predicted RNA-binding protein [General function prediction only]
Probab=98.49 E-value=5.5e-09 Score=125.24 Aligned_cols=80 Identities=18% Similarity=0.042 Sum_probs=72.8
Q ss_pred cccccccccCCCCCCCeEEeeccccchhhhhccCeeeEEeccCCccchh-HHHHHHHHHHhhccCCccccchhccccccc
Q 001312 1017 RLNDVDYLTGNPLPSDILLYVIPVCGPYSAVQSYKYRVKIIPGTAKKGK-GIQIFYSLLLLMLSLTPVFDIFPFQCLCSR 1095 (1102)
Q Consensus 1017 ~~~~ld~Ltg~P~~~D~ll~aiPVcAPy~al~~yKyKvKl~PG~~KKGK-A~k~al~~f~~~~~~~~~~~~l~~~~~~~~ 1095 (1102)
.+...++.++.|.|+|+..+++|||+||+...+|+|.+||+|+-+|||. ||+.++..+++...+|-++.+...-.-+.+
T Consensus 340 e~~~~kAelIe~N~eLVe~~il~I~s~la~~m~W~dieKLik~eqKkGn~vAk~i~~l~l~~n~~t~~L~d~~dd~~de~ 419 (911)
T KOG2030|consen 340 ELNRRKAELIEPNPELVEAAILAIQSALAQQMDWKDIEKLIKSEQKKGNPVAKSIDKLKLEKNEATLRLKDPEDDNDDEK 419 (911)
T ss_pred HHHHHHHHhccCCHHHHHHHHHHHHHHHHccCCcHhHHHHHHHHHhcCchHhhhhhHHHHhhhhheeecCCcccccchhh
Confidence 4566889999999999999999999999999999999999999999999 999999999999999999999888544444
Q ss_pred c
Q 001312 1096 K 1096 (1102)
Q Consensus 1096 ~ 1096 (1102)
+
T Consensus 420 k 420 (911)
T KOG2030|consen 420 K 420 (911)
T ss_pred c
Confidence 4
No 7
>KOG3272 consensus Predicted coiled-coil protein [General function prediction only]
Probab=97.32 E-value=0.00065 Score=70.27 Aligned_cols=89 Identities=19% Similarity=0.293 Sum_probs=69.6
Q ss_pred ecCCceEEecCCchhhHHHHHhhcCCCcEEEEecCCCCcEEEEeCCCCCC---CCCHHHHHHHHHHHhHhcccc-cCCCc
Q 001312 565 SSENYLVISGRDAQQNEMIVKRYMSKGDVYVHADLHGASSTVIKNHRPEQ---PVPPLTLNQAGCFTVCHSQAW-DSKMV 640 (1102)
Q Consensus 565 SSdGylVi~GRda~QNE~Lv~ky~~~~Diw~HAdi~GAshVIIK~~~~~~---~ip~~tL~eAA~lAa~ySkAw-~s~~v 640 (1102)
+...|.++.|+|-..|+.|. +|.-+.|+|||++---++||.|+-. +++ .||...|.++|+|+=.-|--- .-..|
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 6999999999996666678888875 344 589999999999998888543 22234
Q ss_pred ceeEEEeceeccccCC
Q 001312 641 TSAWWVYPHQVSKTAP 656 (1102)
Q Consensus 641 ~~a~wV~~~QVsK~ap 656 (1102)
. +-|+.-+...||+-
T Consensus 88 ~-VvYT~w~NLKKt~~ 102 (207)
T KOG3272|consen 88 E-VVYTPWSNLKKTAD 102 (207)
T ss_pred e-EEechhHhhcccCC
Confidence 4 34477778888763
No 8
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=97.28 E-value=0.0039 Score=76.81 Aligned_cols=121 Identities=21% Similarity=0.237 Sum_probs=93.5
Q ss_pred cccccccHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 001312 347 EFVKFETFDAALDEFYSKI-ESQRAEQQHKAKEDAAFHKLNKIHMDQENRVHTLKQEVDRSVKMAELIEYNLEDVDAAIL 425 (1102)
Q Consensus 347 ~~~~f~sfn~avDeffs~~-e~qk~~~~~~~~e~~~~kKLek~~~~qe~ri~~L~~~~e~~~~kaeLI~aN~~~V~~ai~ 425 (1102)
+...|++++..+++||... ...++.+... .+.+++++.+..+++.++.++++.+.++..++......+.|-.-+.
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 4456788889899998874 5555555444 4778888888899999999999999999999999998888876665
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHHcCCCcccccccccccCceEEEEccCCCCCCcccccCCCcEEEEeCCCCCHHHHHHH
Q 001312 426 AVRVALANRMSWEDLARMVKEERKAGNPVAGLIDKLYLERNCMSLLLSNNLDEMDDEEKTLPVEKVEVDLALSAHANARR 505 (1102)
Q Consensus 426 ~v~~~~a~g~~W~~i~~li~~~~~~gnpvA~~I~~l~l~~n~itl~L~d~~d~~~~~~~~~~~~~I~LDl~lS~~~NA~~ 505 (1102)
.|...+. .+.+.++++ .+.+.|.+|+..++.+|+++
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 233355333 24599999999999999999
Q ss_pred HHHHHHHhHH
Q 001312 506 WYELKKKQES 515 (1102)
Q Consensus 506 YY~k~Kka~~ 515 (1102)
||..+++++.
T Consensus 368 ~~~~~~klk~ 377 (564)
T COG1293 368 YFKKYKKLKG 377 (564)
T ss_pred HhhhhhhccC
Confidence 9999999974
No 9
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=95.88 E-value=0.25 Score=55.86 Aligned_cols=51 Identities=20% Similarity=0.343 Sum_probs=42.9
Q ss_pred hhHHHHH---hhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHH
Q 001312 238 PTLKTVL---GEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKF 291 (1102)
Q Consensus 238 ~~lk~~L---~~~~g~gp~laeei~~~agi~~~~~~~~~~~l~~~~~~~L~~al~~~ 291 (1102)
..++.+| ..+.|+|..+++|+|++|||.|..+.. .|+++++..|+.++..+
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 567799999999999999999998776 58999999999886544
No 10
>PRK10445 endonuclease VIII; Provisional
Probab=95.16 E-value=0.29 Score=54.94 Aligned_cols=50 Identities=24% Similarity=0.428 Sum_probs=39.6
Q ss_pred hHHHHH-hh--hcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHH
Q 001312 239 TLKTVL-GE--ALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKF 291 (1102)
Q Consensus 239 ~lk~~L-~~--~~g~gp~laeei~~~agi~~~~~~~~~~~l~~~~~~~L~~al~~~ 291 (1102)
.++.+| .. +.|+|..+++|+|++|||.|..+.. .|+++++..|+.++..+
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 32 4499999999999999999998765 58999999999886544
No 11
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=94.49 E-value=0.74 Score=51.93 Aligned_cols=50 Identities=16% Similarity=0.206 Sum_probs=40.0
Q ss_pred hHHHHHh---hhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHH
Q 001312 239 TLKTVLG---EALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKF 291 (1102)
Q Consensus 239 ~lk~~L~---~~~g~gp~laeei~~~agi~~~~~~~~~~~l~~~~~~~L~~al~~~ 291 (1102)
.++.+|. .+.|+|..+++|+|++|||.|..+.. .|+++++..|+.++..+
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 24599999999999999999998766 58999999998886543
No 12
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=94.47 E-value=1.3 Score=50.46 Aligned_cols=50 Identities=20% Similarity=0.361 Sum_probs=40.2
Q ss_pred hHHHHHh---hhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHH
Q 001312 239 TLKTVLG---EALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKF 291 (1102)
Q Consensus 239 ~lk~~L~---~~~g~gp~laeei~~~agi~~~~~~~~~~~l~~~~~~~L~~al~~~ 291 (1102)
.++.+|. .+.|+|..++.|+|++|||.|..+.. .|+++++..|+.++..+
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 4555543 24599999999999999999998766 58999999999886544
No 13
>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=94.41 E-value=1.1 Score=50.51 Aligned_cols=50 Identities=20% Similarity=0.359 Sum_probs=40.2
Q ss_pred hHHHHHh---hhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHH
Q 001312 239 TLKTVLG---EALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKF 291 (1102)
Q Consensus 239 ~lk~~L~---~~~g~gp~laeei~~~agi~~~~~~~~~~~l~~~~~~~L~~al~~~ 291 (1102)
.++.+|. .+.|+|..++.|+|++|||.|..+.. .|+++++..|+.++..+
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 4555553 24599999999999999999998766 58999999999886544
No 14
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=92.42 E-value=4.9 Score=45.35 Aligned_cols=41 Identities=20% Similarity=0.356 Sum_probs=34.2
Q ss_pred hcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHH
Q 001312 247 ALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAK 290 (1102)
Q Consensus 247 ~~g~gp~laeei~~~agi~~~~~~~~~~~l~~~~~~~L~~al~~ 290 (1102)
..|+|..++.|+|+++||.|..+.. .++..++..|++++..
T Consensus 168 vaGvGNIYa~E~Lf~agI~P~~~a~---~l~~~~~~~l~~~i~~ 208 (273)
T COG0266 168 VAGVGNIYADEILFRAGIHPARPAG---DLSLAQLALLHEAIKD 208 (273)
T ss_pred eecccHHHHHHHHHHcCCCcccCcc---ccCHHHHHHHHHHHHH
Confidence 4599999999999999999988765 4788888888877543
No 15
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=87.99 E-value=0.87 Score=51.47 Aligned_cols=51 Identities=20% Similarity=0.326 Sum_probs=42.0
Q ss_pred hhHHHHHhhh---cCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHH
Q 001312 238 PTLKTVLGEA---LGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKF 291 (1102)
Q Consensus 238 ~~lk~~L~~~---~g~gp~laeei~~~agi~~~~~~~~~~~l~~~~~~~L~~al~~~ 291 (1102)
..++.+|..- .|+|..+++|+|++|||+|..+.. .+++.++..|+.++..+
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 3567776643 699999999999999999998776 58899999999886543
No 16
>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=87.40 E-value=0.9 Score=42.95 Aligned_cols=50 Identities=22% Similarity=0.391 Sum_probs=36.9
Q ss_pred hHHHHHh---hhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHH
Q 001312 239 TLKTVLG---EALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKF 291 (1102)
Q Consensus 239 ~lk~~L~---~~~g~gp~laeei~~~agi~~~~~~~~~~~l~~~~~~~L~~al~~~ 291 (1102)
.++.+|. .+.|+|..++.|+|+++|+.|..++. .+++.++..|+.++..+
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 4555543 35599999999999999999998876 58899999998886543
No 17
>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=81.21 E-value=3.8 Score=39.84 Aligned_cols=49 Identities=24% Similarity=0.365 Sum_probs=40.8
Q ss_pred hhHHHHHhhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHH
Q 001312 238 PTLKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVA 289 (1102)
Q Consensus 238 ~~lk~~L~~~~g~gp~laeei~~~agi~~~~~~~~~~~l~~~~~~~L~~al~ 289 (1102)
..+..+|....|+|+..+..+|..+|++++.++. .|+++++..|...|.
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 3577889999999999999999999999998876 588999888766544
No 18
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=79.08 E-value=2.1 Score=42.62 Aligned_cols=48 Identities=19% Similarity=0.332 Sum_probs=40.5
Q ss_pred hHHHHHhhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHH
Q 001312 239 TLKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVA 289 (1102)
Q Consensus 239 ~lk~~L~~~~g~gp~laeei~~~agi~~~~~~~~~~~l~~~~~~~L~~al~ 289 (1102)
.+..+|..+.|+|+..+..+|..+|++++.++. .|+++++..|...|.
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 345567888999999999999999999999877 588999988776654
No 19
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=79.04 E-value=1.3e+02 Score=37.52 Aligned_cols=51 Identities=33% Similarity=0.406 Sum_probs=43.3
Q ss_pred hhHHHHHhh-hcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHHHH
Q 001312 238 PTLKTVLGE-ALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVAKF 291 (1102)
Q Consensus 238 ~~lk~~L~~-~~g~gp~laeei~~~agi~~~~~~~~~~~l~~~~~~~L~~al~~~ 291 (1102)
.++..+|.. |..+|+..+++++..+|+++++++. .|+.+++.+|+++|+.+
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 456666665 5599999999999999999998887 48899999999998876
No 20
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=78.84 E-value=2.9 Score=41.26 Aligned_cols=47 Identities=21% Similarity=0.341 Sum_probs=39.8
Q ss_pred HHHHHhhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHH
Q 001312 240 LKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVA 289 (1102)
Q Consensus 240 lk~~L~~~~g~gp~laeei~~~agi~~~~~~~~~~~l~~~~~~~L~~al~ 289 (1102)
+.-+|..+.|+|...+.++|..+|++++..+. +|+++++..|-+++.
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 34457778899999999999999999998877 599999988877654
No 21
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=78.69 E-value=1.8 Score=43.10 Aligned_cols=48 Identities=17% Similarity=0.352 Sum_probs=40.6
Q ss_pred hHHHHHhhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHH
Q 001312 239 TLKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVA 289 (1102)
Q Consensus 239 ~lk~~L~~~~g~gp~laeei~~~agi~~~~~~~~~~~l~~~~~~~L~~al~ 289 (1102)
.+..+|..+.|+|+..+..+|..+|++++.++. .|+++++..|...|.
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 345567888999999999999999999998877 588999988877664
No 22
>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=74.99 E-value=2.6 Score=41.48 Aligned_cols=47 Identities=15% Similarity=0.364 Sum_probs=39.9
Q ss_pred hHHHHHhhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHH
Q 001312 239 TLKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAV 288 (1102)
Q Consensus 239 ~lk~~L~~~~g~gp~laeei~~~agi~~~~~~~~~~~l~~~~~~~L~~al 288 (1102)
.+..+|..+.|+|+..+..+|..+|++++.++. .|+++++..|...|
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 345567888899999999999999999998877 58899998877665
No 23
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=72.72 E-value=4.7 Score=41.82 Aligned_cols=46 Identities=15% Similarity=0.226 Sum_probs=38.3
Q ss_pred HHHHHhhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHH
Q 001312 240 LKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAV 288 (1102)
Q Consensus 240 lk~~L~~~~g~gp~laeei~~~agi~~~~~~~~~~~l~~~~~~~L~~al 288 (1102)
+..+|..+.|+|+..|..+|..+|++++.++. +|+++++..|...|
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 44557778899999999999999999998877 58899988765553
No 24
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=69.14 E-value=7.1 Score=40.30 Aligned_cols=47 Identities=30% Similarity=0.364 Sum_probs=38.8
Q ss_pred hHHHHHhhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHH
Q 001312 239 TLKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAV 288 (1102)
Q Consensus 239 ~lk~~L~~~~g~gp~laeei~~~agi~~~~~~~~~~~l~~~~~~~L~~al 288 (1102)
.+..+|..+.|+|+..+..+|..+|++++.++. +|+++++..|...|
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 344557788899999999999999999998877 58899988765553
No 25
>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=66.62 E-value=7.9 Score=39.77 Aligned_cols=47 Identities=32% Similarity=0.408 Sum_probs=39.0
Q ss_pred HHHHHhhhcCCCHHHHHHHHHHcCCCCCCcccccccCCHHHHHHHHHHHH
Q 001312 240 LKTVLGEALGYGPALSEHIILDTGLVPNMKLSEVNKLEDNAIQVLVLAVA 289 (1102)
Q Consensus 240 lk~~L~~~~g~gp~laeei~~~agi~~~~~~~~~~~l~~~~~~~L~~al~ 289 (1102)
+..+|..+.|+|+..+..+|.++|++++.++. +|+++++..|...|.
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 44557788899999999999999999998877 588999888765543
No 26
>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]
Probab=52.44 E-value=2.9e+02 Score=28.64 Aligned_cols=38 Identities=16% Similarity=0.254 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Q 001312 395 RVHTLKQEVDRSVKMAELIEYNLEDVDAAILAVRVALA 432 (1102)
Q Consensus 395 ri~~L~~~~e~~~~kaeLI~aN~~~V~~ai~~v~~~~a 432 (1102)
.++.|..+...+....+.|.+.+..+..++.-++.+++
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 34455555556666666777777777777766666654
No 27
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=51.36 E-value=80 Score=38.86 Aligned_cols=51 Identities=18% Similarity=0.173 Sum_probs=41.1
Q ss_pred hhHHHHHhh-hcCCCHHHHHHHHHHcCCC---CCCcccccccCCHHHHHHHHHHHHHH
Q 001312 238 PTLKTVLGE-ALGYGPALSEHIILDTGLV---PNMKLSEVNKLEDNAIQVLVLAVAKF 291 (1102)
Q Consensus 238 ~~lk~~L~~-~~g~gp~laeei~~~agi~---~~~~~~~~~~l~~~~~~~L~~al~~~ 291 (1102)
.++..+|.. |..+|...+++++..+|++ +++++. .|+.+++.+|+++|+..
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 356666654 5589999999999999988 777665 48899999999998763
No 28
>PF13077 DUF3909: Protein of unknown function (DUF3909)
Probab=39.72 E-value=23 Score=32.66 Aligned_cols=28 Identities=25% Similarity=0.606 Sum_probs=21.4
Q ss_pred HHHHhhcCCC-cEEEEecCCCCcEEEEeC
Q 001312 582 MIVKRYMSKG-DVYVHADLHGASSTVIKN 609 (1102)
Q Consensus 582 ~Lv~ky~~~~-Diw~HAdi~GAshVIIK~ 609 (1102)
+|-.||-+.+ |+|+||.+.|-.||-|--
T Consensus 64 ylalkydrdgi~lym~aeidg~~~vsvsy 92 (108)
T PF13077_consen 64 YLALKYDRDGIDLYMHAEIDGVCYVSVSY 92 (108)
T ss_pred HHhheecccceeEEEEeeeccEEEEEEee
Confidence 3555676655 999999999988887654
No 29
>KOG0407 consensus 40S ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=30.82 E-value=1.5e+02 Score=29.01 Aligned_cols=24 Identities=33% Similarity=0.624 Sum_probs=20.2
Q ss_pred hhcCCCcEEEEe-cCCCCcEEEEeCC
Q 001312 586 RYMSKGDVYVHA-DLHGASSTVIKNH 610 (1102)
Q Consensus 586 ky~~~~Diw~HA-di~GAshVIIK~~ 610 (1102)
=|+..||-|+|. |+.| .-+|+|-.
T Consensus 21 i~asfndtfvhitdlsg-~eti~rvt 45 (139)
T KOG0407|consen 21 IFASFNDTFVHVTDLSG-KETIVRVT 45 (139)
T ss_pred EEeecccceEEEeccCC-ceEEEEec
Confidence 478899999999 9999 56888863
No 30
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=29.01 E-value=1.9e+02 Score=35.22 Aligned_cols=53 Identities=21% Similarity=0.286 Sum_probs=40.9
Q ss_pred chhHHHHHhh-hcCCCHHHHHHHHHHcCCCCCCcccccccCC----HHHHHHHHHHHHHHH
Q 001312 237 QPTLKTVLGE-ALGYGPALSEHIILDTGLVPNMKLSEVNKLE----DNAIQVLVLAVAKFE 292 (1102)
Q Consensus 237 ~~~lk~~L~~-~~g~gp~laeei~~~agi~~~~~~~~~~~l~----~~~~~~L~~al~~~~ 292 (1102)
..+++.+|.. |.-+|-..+++++..+|++++..+. .|. .+++..|+++|++..
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 3466666654 5589999999999999999997765 355 778888888887654
No 31
>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.22 E-value=49 Score=34.22 Aligned_cols=68 Identities=19% Similarity=0.152 Sum_probs=48.8
Q ss_pred eEEecCCchhhHHHHHhhcCCCcEEEEecCCCCcEEEEeC----CCCCCCCCHHHHHHHHHHHhHhcccccCCC
Q 001312 570 LVISGRDAQQNEMIVKRYMSKGDVYVHADLHGASSTVIKN----HRPEQPVPPLTLNQAGCFTVCHSQAWDSKM 639 (1102)
Q Consensus 570 lVi~GRda~QNE~Lv~ky~~~~Diw~HAdi~GAshVIIK~----~~~~~~ip~~tL~eAA~lAa~ySkAw~s~~ 639 (1102)
.|-.|.|+-.+.++ .+++++||-+-+|++=|+.+|=|. ++.|..-.+++|.++=.+-=..-+.+.+|.
T Consensus 48 ~V~~g~DaaD~~Iv--~~a~~gDlVVT~Di~LA~~ll~kg~~v~~prGr~y~~~nI~~~L~~R~~~~~lR~~G~ 119 (150)
T COG1671 48 VVDAGFDAADDWIV--NLAEKGDLVVTADIPLASLLLDKGAAVLNPRGRLYTEENIGERLAMRDFMAKLRRQGK 119 (150)
T ss_pred EecCCcchHHHHHH--HhCCCCCEEEECchHHHHHHHhcCCEEECCCCcccCHhHHHHHHHHHHHHHHHHHhcc
Confidence 46678999999888 799999999999999777654442 125777899999887555444444444443
No 32
>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=26.92 E-value=6.8e+02 Score=25.37 Aligned_cols=49 Identities=10% Similarity=0.235 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 001312 378 EDAAFHKLNKIHMDQENRVHTLKQEVDRSVKMAELIEYNLEDVDAAILA 426 (1102)
Q Consensus 378 e~~~~kKLek~~~~qe~ri~~L~~~~e~~~~kaeLI~aN~~~V~~ai~~ 426 (1102)
...+...|...++++..||+.|...+++.......|......|..=+..
T Consensus 52 l~~vs~~l~~tKkhLsqRId~vd~klDe~~ei~~~i~~eV~~v~~dv~~ 100 (126)
T PF07889_consen 52 LEQVSESLSSTKKHLSQRIDRVDDKLDEQKEISKQIKDEVTEVREDVSQ 100 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhHHH
Confidence 3445566777777777778777777777777666666666555543333
No 33
>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=26.39 E-value=1.1e+02 Score=26.77 Aligned_cols=30 Identities=27% Similarity=0.375 Sum_probs=24.7
Q ss_pred ceeEEEeeCCCeEEEEEEeeCCceEEEEEEec
Q 001312 94 RLEDVRQLGYDRIILFQFGLGMNAHYVILELY 125 (1102)
Q Consensus 94 RL~~V~Q~g~DRII~~~F~~G~~~~~LilEL~ 125 (1102)
|-..|....-|+.|+|.|+-|+ =.|.|||+
T Consensus 10 ryVRv~~~~~~gfVEFeFaIG~--PeL~VELv 39 (59)
T PF06099_consen 10 RYVRVTGRRDDGFVEFEFAIGD--PELFVELV 39 (59)
T ss_pred CEEEEecccCCCeEEEEEecCC--cceeEEec
Confidence 4455777889999999999996 47999986
No 34
>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=24.84 E-value=8.5e+02 Score=25.82 Aligned_cols=37 Identities=16% Similarity=0.192 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Q 001312 499 AHANARRWYELKKKQESKQEKTITAHSKAFKAAEKKT 535 (1102)
Q Consensus 499 ~~~NA~~YY~k~Kka~~K~ekt~~a~~kalk~aEkk~ 535 (1102)
..++...|+++.++.+.-.+|..++.-..++...+.+
T Consensus 123 ~eEtv~~~ieqqk~~r~e~qk~~~~yv~~~k~~q~~~ 159 (165)
T PF09602_consen 123 YEETVKQLIEQQKLTREEWQKVLDAYVEQAKSSQKEL 159 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3467778888887776666666666666555555443
No 35
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=22.95 E-value=66 Score=41.52 Aligned_cols=13 Identities=8% Similarity=0.378 Sum_probs=7.2
Q ss_pred ccHHHHHHHHHHH
Q 001312 352 ETFDAALDEFYSK 364 (1102)
Q Consensus 352 ~sfn~avDeffs~ 364 (1102)
.+.+..|-+||..
T Consensus 1013 ~sLdSIVt~Ylr~ 1025 (1516)
T KOG1832|consen 1013 LSLDSIVTQYLRH 1025 (1516)
T ss_pred CcHHHHHHHHHHH
Confidence 3555566666643
No 36
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=21.95 E-value=30 Score=32.53 Aligned_cols=16 Identities=44% Similarity=0.605 Sum_probs=13.4
Q ss_pred ccccccCCCCCCCeEE
Q 001312 1020 DVDYLTGNPLPSDILL 1035 (1102)
Q Consensus 1020 ~ld~Ltg~P~~~D~ll 1035 (1102)
.|-++||+|+|.|.=|
T Consensus 62 FLHA~TGQPLP~D~Dl 77 (105)
T PRK05264 62 FLHAFTGQPLPDDEDL 77 (105)
T ss_pred HHHHHcCCCCCChhhh
Confidence 4789999999999654
No 37
>cd00490 Met_repressor_MetJ Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ forms sufficiently strong interactions with the sugar-phosphate backbone to accomodate sequence variation in natural operators. However, it is very sensitive to particular base changes in the operator. MetJ exists as a homodimer.
Probab=21.55 E-value=32 Score=32.07 Aligned_cols=16 Identities=44% Similarity=0.644 Sum_probs=13.4
Q ss_pred ccccccCCCCCCCeEE
Q 001312 1020 DVDYLTGNPLPSDILL 1035 (1102)
Q Consensus 1020 ~ld~Ltg~P~~~D~ll 1035 (1102)
.|-++||+|+|.|.=|
T Consensus 61 FLHAfTGQPLP~D~Dl 76 (103)
T cd00490 61 FLHAFTGQPLPDDADL 76 (103)
T ss_pred HHHHhcCCCCCChhhh
Confidence 4789999999999654
No 38
>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=20.65 E-value=5.1e+02 Score=22.90 Aligned_cols=14 Identities=36% Similarity=0.681 Sum_probs=11.0
Q ss_pred ccHHHHHHHHHHHH
Q 001312 352 ETFDAALDEFYSKI 365 (1102)
Q Consensus 352 ~sfn~avDeffs~~ 365 (1102)
..|..++|.||...
T Consensus 5 ~~F~~a~~~~~~~~ 18 (77)
T PF03993_consen 5 KRFRAACDAFFDRR 18 (77)
T ss_pred HHHHHHHHHHHHHH
Confidence 35889999999764
No 39
>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=20.25 E-value=3.7e+02 Score=26.11 Aligned_cols=45 Identities=20% Similarity=0.267 Sum_probs=25.2
Q ss_pred cccHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001312 351 FETFDAALDEFYSK-IESQRAEQQHKAKEDAAFHKLNKIHMDQENRVHTLKQEV 403 (1102)
Q Consensus 351 f~sfn~avDeffs~-~e~qk~~~~~~~~e~~~~kKLek~~~~qe~ri~~L~~~~ 403 (1102)
|.....|-+++|-. .+. ++.+.++.+|++-+..|++.|+.|++..
T Consensus 54 f~krE~A~E~~Y~r~~Ek--------EqL~~Lk~kl~~e~~~~~k~i~~le~~I 99 (100)
T PF04568_consen 54 FGKREAAQEEQYFRKKEK--------EQLKKLKEKLKEEIEHHRKEIDELEKHI 99 (100)
T ss_dssp HHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cchHHHhhHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 44444555554432 232 2334556666666666777777776543
No 40
>PF04048 Sec8_exocyst: Sec8 exocyst complex component specific domain; InterPro: IPR007191 Sec8 is a component of the exocyst complex involved in the docking of exocystic vesicles with a fusion site on the plasma membrane. The exocyst complex is composed of Sec3, Sec5, Sec6, Sec8, Sec10, Sec15, Exo70 and Exo84.; GO: 0006904 vesicle docking involved in exocytosis, 0015031 protein transport, 0000145 exocyst
Probab=20.19 E-value=6.4e+02 Score=25.68 Aligned_cols=49 Identities=12% Similarity=0.216 Sum_probs=28.0
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001312 350 KFETFDAALDEFYSKIESQRAEQQHKAKEDAAFHKLNKIHMDQENRVHTLKQ 401 (1102)
Q Consensus 350 ~f~sfn~avDeffs~~e~qk~~~~~~~~e~~~~kKLek~~~~qe~ri~~L~~ 401 (1102)
+|..||.+|-.|=.-... -...+.....++..|...+..+..+-..|.+
T Consensus 63 h~q~Fn~sI~sy~~i~~~---i~~sq~~i~~lK~~L~~ak~~L~~~~~eL~~ 111 (142)
T PF04048_consen 63 HYQGFNSSIGSYSQILSS---ISESQERIRELKESLQEAKSLLGCRREELKE 111 (142)
T ss_pred HHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHH
Confidence 467889998876433211 1122334455667777777666665555554
Done!