Query psy4335
Match_columns 152
No_of_seqs 120 out of 1081
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 22:58:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4335.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4335hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00070 40S ribosomal protein 100.0 7.1E-64 1.5E-68 413.4 14.7 148 4-151 44-196 (257)
2 TIGR01020 rpsE_arch ribosomal 100.0 8.7E-62 1.9E-66 393.0 14.7 147 4-151 15-168 (212)
3 PRK04044 rps5p 30S ribosomal p 100.0 7.2E-59 1.6E-63 376.1 14.8 147 4-151 16-168 (211)
4 KOG0877|consensus 100.0 2.2E-57 4.8E-62 363.5 9.0 149 3-151 15-167 (213)
5 COG0098 RpsE Ribosomal protein 100.0 4.3E-45 9.4E-50 288.9 13.9 129 8-151 1-133 (181)
6 CHL00138 rps5 ribosomal protei 100.0 1E-40 2.2E-45 256.6 13.8 108 37-151 22-133 (143)
7 TIGR01021 rpsE_bact ribosomal 100.0 1.9E-39 4.2E-44 252.3 13.1 106 38-151 1-110 (154)
8 PRK00550 rpsE 30S ribosomal pr 100.0 6.2E-39 1.3E-43 252.5 13.3 107 37-151 11-121 (168)
9 PF00333 Ribosomal_S5: Ribosom 99.9 1E-26 2.2E-31 158.5 8.5 67 38-104 1-67 (67)
10 KOG2646|consensus 99.8 5.2E-22 1.1E-26 171.0 2.7 107 38-151 181-294 (396)
11 PF03719 Ribosomal_S5_C: Ribos 98.7 9.8E-09 2.1E-13 71.1 3.4 31 121-151 1-35 (74)
12 smart00358 DSRM Double-strande 65.7 26 0.00057 21.7 5.3 39 57-99 28-66 (67)
13 cd00048 DSRM Double-stranded R 61.0 36 0.00078 20.9 5.9 38 56-97 29-66 (68)
14 PF02294 7kD_DNA_binding: 7kD 54.0 25 0.00055 23.1 3.6 43 40-86 10-52 (62)
15 PF12327 FtsZ_C: FtsZ family, 33.4 50 0.0011 23.3 2.9 24 72-95 3-27 (95)
16 COG3360 Uncharacterized conser 29.9 53 0.0012 22.7 2.4 23 80-102 14-37 (71)
17 PRK13187 UDP-3-O-[3-hydroxymyr 29.2 75 0.0016 27.6 3.8 14 126-139 33-49 (304)
18 PF10957 DUF2758: Protein of u 29.0 1.3E+02 0.0027 20.0 4.0 39 27-66 16-57 (60)
19 PRK13186 lpxC UDP-3-O-[3-hydro 28.3 39 0.00084 29.1 1.9 14 126-139 26-39 (295)
20 PF07311 Dodecin: Dodecin; In 27.2 68 0.0015 21.7 2.5 22 82-103 14-35 (66)
21 PF04098 Rad52_Rad22: Rad52/22 27.2 2.8E+02 0.0061 21.1 7.8 66 32-98 43-122 (154)
22 TIGR00325 lpxC UDP-3-0-acyl N- 26.6 43 0.00094 28.9 1.9 14 126-139 25-38 (297)
23 KOG3438|consensus 26.4 36 0.00079 25.2 1.1 30 115-147 48-78 (105)
24 PRK15184 curli production asse 25.6 1.2E+02 0.0027 26.0 4.4 65 43-108 186-253 (277)
25 PF02624 YcaO: YcaO-like famil 25.5 1.3E+02 0.0028 24.8 4.5 35 69-103 198-232 (332)
26 PHA02701 ORF020 dsRNA-binding 25.2 3.3E+02 0.0071 22.1 6.5 37 56-96 136-172 (183)
27 PRK00102 rnc ribonuclease III; 24.8 2.1E+02 0.0046 22.5 5.5 38 58-99 189-226 (229)
28 COG1153 FwdD Formylmethanofura 24.8 50 0.0011 25.2 1.7 35 98-132 73-110 (128)
29 PF02482 Ribosomal_S30AE: Sigm 24.4 2.3E+02 0.0049 19.0 5.1 29 71-99 59-87 (97)
30 KOG3769|consensus 23.0 22 0.00048 31.1 -0.6 77 17-102 227-304 (333)
31 PF08502 LeuA_dimer: LeuA allo 23.0 1.8E+02 0.004 21.3 4.5 44 55-98 88-131 (133)
32 PF03331 LpxC: UDP-3-O-acyl N- 22.7 55 0.0012 27.9 1.7 13 126-138 25-37 (277)
33 PF09843 DUF2070: Predicted me 22.7 1.9E+02 0.0041 22.6 4.7 46 60-106 112-157 (179)
34 PRK13188 bifunctional UDP-3-O- 22.5 59 0.0013 29.8 2.0 17 123-139 22-40 (464)
35 cd03315 MLE_like Muconate lact 22.0 1.8E+02 0.004 23.5 4.7 32 61-96 25-56 (265)
36 PF13867 SAP30_Sin3_bdg: Sin3 21.9 27 0.00058 22.3 -0.2 14 22-35 36-49 (53)
37 TIGR02191 RNaseIII ribonucleas 20.6 3.3E+02 0.0071 21.2 5.7 37 58-98 183-219 (220)
No 1
>PTZ00070 40S ribosomal protein S2; Provisional
Probab=100.00 E-value=7.1e-64 Score=413.45 Aligned_cols=148 Identities=62% Similarity=0.998 Sum_probs=146.4
Q ss_pred ceeeccCCccCHHHHhhcCCCCCchhhhhcccC-CCccceeEEEeeeeeeecCCeeEEEEEEEEecCCCceEEeeeecch
Q psy4335 4 CLAFRDGKIQSLEQIYLFSLPIKEFEIIDFFIG-SSLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSK 82 (152)
Q Consensus 4 ~~~vk~~~i~~~~~~~~~~l~i~e~eiid~~~~-~~l~~~vl~i~rV~k~tk~Gr~~rf~alVvvGn~nG~vG~G~gks~ 82 (152)
|||||||||+||||||+|||||+|+||||+||+ ++|+|+||+|+||||||++||++||+|||+|||+||+||||++||+
T Consensus 44 GrlVk~gki~s~eei~~~~lpikE~eIvd~ll~~~~L~eeVl~I~rVqK~TkgGrr~rF~AlVVVGd~nG~VGlG~gKak 123 (257)
T PTZ00070 44 GRLVKAGKITSLEEIFLFSIPIKEYQIVDHFFAESKLKDEVMKIMPVQKQTSAGQRTRFKAFVVVGDGNGHIGLGAKVAK 123 (257)
T ss_pred hhhhhcCccccHHHHHhcCCCccchhhHHHHccCccchheEEEEeeeEEEecCCcEEEEEEEEEEeCCCCcEecceeech
Confidence 899999999999999999999999999999996 8999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHhhcceeeeecccCCcCCCCceeeeeeeee-e---EEEeecCCCcceeeChhhHHhhcccC
Q psy4335 83 EVATAIRGAIILAKLSVVPVRRGYWGNKIGKPHTVPCKRLTH-G---DQQIPGGRKSKVLSSPENLKVTSTSK 151 (152)
Q Consensus 83 ev~~Ai~kA~~~Ak~nli~v~rgy~~~~~~~~hTI~~~v~gk-g---V~l~Pap~GtGiva~~~~k~il~lAg 151 (152)
||++||+||+.+|++||++|+|+||+|+++++|||||+++|| | |.|+|||+||||+|++++++||+|||
T Consensus 124 EV~~AIrKAi~~AK~nii~V~rgyW~~~~g~~hTIp~~V~GK~GSv~V~L~PAP~GtGivAg~~vk~VLelAG 196 (257)
T PTZ00070 124 EVATAIRGAIIAAKLNLVPVRRGYWGNKIGEPHTVPMKVTGKCGSVRVRLVPAPRGTGIVAAPTPKKILEFAG 196 (257)
T ss_pred hHHHHHHHHHHHHHhCeEEEecccccccCCCCCCeeeeEEEEeCeEEEEEEeCCCCccEEeCcHHHHHHHHcC
Confidence 999999999999999999999999999999999999999999 6 99999999999999999999999998
No 2
>TIGR01020 rpsE_arch ribosomal protein S5(archaeal type)/S2(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S2 as well as archaeal ribosomal protein S5.
Probab=100.00 E-value=8.7e-62 Score=392.98 Aligned_cols=147 Identities=44% Similarity=0.738 Sum_probs=144.9
Q ss_pred ceeeccCCccCHHHHhhcCCCCCchhhhhcccCCCc-cceeEEEeeeeeeecCCeeEEEEEEEEecCCCceEEeeeecch
Q psy4335 4 CLAFRDGKIQSLEQIYLFSLPIKEFEIIDFFIGSSL-KDEVLKIMPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSK 82 (152)
Q Consensus 4 ~~~vk~~~i~~~~~~~~~~l~i~e~eiid~~~~~~l-~~~vl~i~rV~k~tk~Gr~~rf~alVvvGn~nG~vG~G~gks~ 82 (152)
|||||||||+||||||.||+||+|+||||+|| ++| +|+||+|+||||||++||++||+|||+|||+||++|||+|||+
T Consensus 15 grlV~~g~i~s~~ei~~~~~~i~E~eivd~ll-~~l~~e~vl~I~rV~K~tkgGr~~~F~alVvVGn~~G~vG~G~GKa~ 93 (212)
T TIGR01020 15 GRLVKEGKIKSIDEIFLRNLPIKEPEIVDYLL-PDLNEEEVLDVSLVQRMTDSGRRTRFRAFVVVGNRDGYVGLGIGKAK 93 (212)
T ss_pred hhhhhcCCcccHHHHHHcCCCccchhhHHHHh-hhcCcceEEEEEeeEEEecCCcEEEEEEEEEEeCCCCeEeeceeecc
Confidence 89999999999999999999999999999999 599 8899999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHhhcceeeee--cccCCcCCCCceeeeeeeee-e---EEEeecCCCcceeeChhhHHhhcccC
Q psy4335 83 EVATAIRGAIILAKLSVVPVRR--GYWGNKIGKPHTVPCKRLTH-G---DQQIPGGRKSKVLSSPENLKVTSTSK 151 (152)
Q Consensus 83 ev~~Ai~kA~~~Ak~nli~v~r--gy~~~~~~~~hTI~~~v~gk-g---V~l~Pap~GtGiva~~~~k~il~lAg 151 (152)
|+++||++|+.+|++||++|+| |||+|.|+++|||||+++|| | |.|+|||+|+||+|+++++++|+|||
T Consensus 94 ev~~AI~kA~~~Ak~n~i~V~rg~g~w~~~~~~~hTIp~~v~Gk~gs~~V~L~PAP~GtGliag~~~r~ilelAG 168 (212)
T TIGR01020 94 EVAPAIRKAIINAKLNIIPVRRGCGSWECGCGRPHSVPFKVTGKCGSVRVRLIPAPRGLGLVAGDVAKKVLRLAG 168 (212)
T ss_pred hHHHHHHHHHHHHHhCEEEEecccccccccCCCCCcEeEEEEEEEccEEEEEEeCCCCCceecCcHHHHHHHHcC
Confidence 9999999999999999999999 89999999999999999999 6 99999999999999999999999998
No 3
>PRK04044 rps5p 30S ribosomal protein S5P; Reviewed
Probab=100.00 E-value=7.2e-59 Score=376.11 Aligned_cols=147 Identities=39% Similarity=0.607 Sum_probs=145.0
Q ss_pred ceeeccCCccCHHHHhhcCCCCCchhhhhcccCCCccceeEEEeeeeeeecCCeeEEEEEEEEecCCCceEEeeeecchh
Q psy4335 4 CLAFRDGKIQSLEQIYLFSLPIKEFEIIDFFIGSSLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSKE 83 (152)
Q Consensus 4 ~~~vk~~~i~~~~~~~~~~l~i~e~eiid~~~~~~l~~~vl~i~rV~k~tk~Gr~~rf~alVvvGn~nG~vG~G~gks~e 83 (152)
|||||||+|+||||||.+|+||+|+||||+|| ++|+|+||+++||||||++||++||+|||+|||+||++|||+|||+|
T Consensus 16 g~lv~~~~i~s~e~i~~~~~~i~e~eivd~ll-~~l~e~vv~i~rV~kvtkgGr~~sf~alVvVGn~~G~vG~G~GKa~e 94 (211)
T PRK04044 16 GRLVKEGKITSIDEIFDSGLPIKEPEIVDVLL-PDLEDEVLDINMVQRMTDSGRRVRFRVVVVVGNRDGYVGVGQGKAKQ 94 (211)
T ss_pred hhhhhcCCcccHHHHHhcCCCcccchhhhhhh-ccceeEEEEEEeEEeeecCCcEEEEEEEEEEeCCCCeEeeeeeeccc
Confidence 89999999999999999999999999999999 79999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhcceeeeec--ccCCcCCCCceeeeeeeee-e---EEEeecCCCcceeeChhhHHhhcccC
Q psy4335 84 VATAIRGAIILAKLSVVPVRRG--YWGNKIGKPHTVPCKRLTH-G---DQQIPGGRKSKVLSSPENLKVTSTSK 151 (152)
Q Consensus 84 v~~Ai~kA~~~Ak~nli~v~rg--y~~~~~~~~hTI~~~v~gk-g---V~l~Pap~GtGiva~~~~k~il~lAg 151 (152)
+++||+||+.+|++||++|+|+ ||||.|+++|||||+++|| | |+|+|||+||||+|++.+++||++||
T Consensus 95 v~~Ai~kA~~~Akknli~V~r~~g~We~~~~~~~TI~h~v~gk~gs~~V~l~Pap~GtGiiag~~vr~vlelaG 168 (211)
T PRK04044 95 VGPAIRKAIRNAKLNIIKVRRGCGSWECGCGEPHSVPFKVTGKAGSVEVTLKPAPRGLGLVAGDVAKKVLELAG 168 (211)
T ss_pred hHHHHHHHHHHHHhCeEEEEcccccccccCCCCCcCCeEEEEEEccEEEEEEECCCCCeEEECcHHHHHHHHcC
Confidence 9999999999999999999995 8999999999999999999 6 99999999999999999999999998
No 4
>KOG0877|consensus
Probab=100.00 E-value=2.2e-57 Score=363.53 Aligned_cols=149 Identities=74% Similarity=1.108 Sum_probs=147.4
Q ss_pred cceeeccCCccCHHHHhhcCCCCCchhhhhcccCCCccceeEEEeeeeeeecCCeeEEEEEEEEecCCCceEEeeeecch
Q psy4335 3 QCLAFRDGKIQSLEQIYLFSLPIKEFEIIDFFIGSSLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSK 82 (152)
Q Consensus 3 ~~~~vk~~~i~~~~~~~~~~l~i~e~eiid~~~~~~l~~~vl~i~rV~k~tk~Gr~~rf~alVvvGn~nG~vG~G~gks~ 82 (152)
-|++|++|||+|+||||+|||||+|+||||||++.+|+|+||+|++|||||++||++||+|+|++||+||+||+|+.|++
T Consensus 15 lG~lv~~~ki~sleeiyl~slpike~eiid~~lg~slkdeVLkImpVqKqtrAGQrtRfKAfVaigD~~ghVGlgvk~sK 94 (213)
T KOG0877|consen 15 LGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSK 94 (213)
T ss_pred ccccchhchhhhhhhhhccCccccchhhhhhhhccchHhhhheeeecccccccccccceEEEEEEeecCCceeeeeeehH
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHhhcceeeeecccCCcCCCCceeeeeeeee-e---EEEeecCCCcceeeChhhHHhhcccC
Q psy4335 83 EVATAIRGAIILAKLSVVPVRRGYWGNKIGKPHTVPCKRLTH-G---DQQIPGGRKSKVLSSPENLKVTSTSK 151 (152)
Q Consensus 83 ev~~Ai~kA~~~Ak~nli~v~rgy~~~~~~~~hTI~~~v~gk-g---V~l~Pap~GtGiva~~~~k~il~lAg 151 (152)
|+++||++|+.+|+++++||+|+||+|++++|||+||+++|+ + |.++|||||+||++.|+++++|+|||
T Consensus 95 eva~airgaiilaklsivpvrrgyw~~~~g~pHt~~~kvtg~~~svlv~l~papRgtGivs~p~~kkll~mAG 167 (213)
T KOG0877|consen 95 EVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGDCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAG 167 (213)
T ss_pred HHHHHHhHHHhhhheeeeeeeccccccccCCCccccCcccccCCcceEEEeecCCCCceeeccccHHHHHhcc
Confidence 999999999999999999999999999999999999999999 6 99999999999999999999999998
No 5
>COG0098 RpsE Ribosomal protein S5 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.3e-45 Score=288.94 Aligned_cols=129 Identities=36% Similarity=0.563 Sum_probs=122.9
Q ss_pred ccCCccCHHHHhhcCCCCCchhhhhcccCCCccceeEEEeeeeeeecCCeeEEEEEEEEecCCCceEEeeeecchhHHHH
Q psy4335 8 RDGKIQSLEQIYLFSLPIKEFEIIDFFIGSSLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSKEVATA 87 (152)
Q Consensus 8 k~~~i~~~~~~~~~~l~i~e~eiid~~~~~~l~~~vl~i~rV~k~tk~Gr~~rf~alVvvGn~nG~vG~G~gks~ev~~A 87 (152)
+++++.+++ |..++|++|+| +|. |.+++|+|+||||||++||++||+|||+|||+||+||||.||++||+.|
T Consensus 1 ~~~~~~~~~--~~~~~~~~e~~-~~~-----l~e~vv~inrV~K~~kgGRr~~F~alvVVGd~~G~VG~G~GKA~EV~~A 72 (181)
T COG0098 1 KEGKIATIE--FKSGLPIKEPE-VDE-----LLEKVVDINRVSKVVKGGRRFRFSALVVVGDRNGRVGFGIGKAKEVPEA 72 (181)
T ss_pred CCccccchh--hhhccCcCCch-hhh-----cceeeeEEEEEEEeecCceEEEEEEEEEEeCCCCeEeeeecchhhhHHH
Confidence 468899997 99999999999 774 4588999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhcceeeeecccCCcCCCCceeeeeeeee-e---EEEeecCCCcceeeChhhHHhhcccC
Q psy4335 88 IRGAIILAKLSVVPVRRGYWGNKIGKPHTVPCKRLTH-G---DQQIPGGRKSKVLSSPENLKVTSTSK 151 (152)
Q Consensus 88 i~kA~~~Ak~nli~v~rgy~~~~~~~~hTI~~~v~gk-g---V~l~Pap~GtGiva~~~~k~il~lAg 151 (152)
|+||+..|++||++|+|+ ++|||||++.|+ | |+|+|||+||||+|++++|+||||||
T Consensus 73 IrKAi~~Ak~nii~V~~~-------~~~Tiph~v~Gk~g~~~V~L~PA~~GtGiiAGg~~r~vlelAG 133 (181)
T COG0098 73 IRKAIEDAKKNIIEVPRG-------NGHTIPHEVIGKHGAVKVLLKPAPEGTGIIAGGAVRAVLELAG 133 (181)
T ss_pred HHHHHHHHHhCeEEEecC-------CCceeeeEEEEEECcEEEEEEECCCCceEEeCcHHHHHHHHcC
Confidence 999999999999999995 679999999999 6 99999999999999999999999998
No 6
>CHL00138 rps5 ribosomal protein S5; Validated
Probab=100.00 E-value=1e-40 Score=256.64 Aligned_cols=108 Identities=25% Similarity=0.398 Sum_probs=105.4
Q ss_pred CCccceeEEEeeeeeeecCCeeEEEEEEEEecCCCceEEeeeecchhHHHHHHHHHHHHhhcceeeeecccCCcCCCCce
Q psy4335 37 SSLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVRRGYWGNKIGKPHT 116 (152)
Q Consensus 37 ~~l~~~vl~i~rV~k~tk~Gr~~rf~alVvvGn~nG~vG~G~gks~ev~~Ai~kA~~~Ak~nli~v~rgy~~~~~~~~hT 116 (152)
++|+|++|+++||||||++||++||+|||+|||+||++|+|+||++|+++||++|+.+|++||++|+|+ ++||
T Consensus 22 ~~l~ekvl~i~rV~k~tkgGR~~~f~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknl~~V~~~-------~~~T 94 (143)
T CHL00138 22 NKWEERVIQIKRVSKVVKGGKKLSFRAIVVIGNENGWVGVGVGKADDVQNAVKKAVTDAKKNLITIPLT-------KSNS 94 (143)
T ss_pred CCceEEEEEEeeeeEEecCCcEEEEEEEEEEECCCCeEEEeeEecchHHHHHHHHHHHHHhCeEEEEcC-------CCCe
Confidence 789999999999999999999999999999999999999999999999999999999999999999995 5699
Q ss_pred eeeeeeee-e---EEEeecCCCcceeeChhhHHhhcccC
Q psy4335 117 VPCKRLTH-G---DQQIPGGRKSKVLSSPENLKVTSTSK 151 (152)
Q Consensus 117 I~~~v~gk-g---V~l~Pap~GtGiva~~~~k~il~lAg 151 (152)
|||+++|| + |.|+|||+|+||+|++.++++|++||
T Consensus 95 I~~~v~gk~gs~~V~l~Pap~G~Gi~a~~~i~~vlelaG 133 (143)
T CHL00138 95 IPHNITGIFGAAKVILRPSAPGSGVIAGGSVRIVLELAG 133 (143)
T ss_pred EeeEEEEEEeeEEEEEEECCCCCcEEECcHHHHHHHHcC
Confidence 99999999 6 99999999999999999999999998
No 7
>TIGR01021 rpsE_bact ribosomal protein S5, bacterial/organelle type. This model finds chloroplast ribosomal protein S5 as well as bacterial ribosomal protein S5. A candidate mitochondrial form (Saccharomyces cerevisiae YBR251W and its homolog) differs substantially and is not included in this model.
Probab=100.00 E-value=1.9e-39 Score=252.27 Aligned_cols=106 Identities=25% Similarity=0.413 Sum_probs=102.7
Q ss_pred CccceeEEEeeeeeeecCCeeEEEEEEEEecCCCceEEeeeecchhHHHHHHHHHHHHhhcceeeeecccCCcCCCCcee
Q psy4335 38 SLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVRRGYWGNKIGKPHTV 117 (152)
Q Consensus 38 ~l~~~vl~i~rV~k~tk~Gr~~rf~alVvvGn~nG~vG~G~gks~ev~~Ai~kA~~~Ak~nli~v~rgy~~~~~~~~hTI 117 (152)
+|+|++|+++||||||++||++||+|+|+|||+||++|+|+||++|+++||++|+.+|++||++|+|+ ++ ||
T Consensus 1 ~l~e~vl~i~rv~k~tkgGr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~kA~~~Ak~nl~~V~~~-------~~-Ti 72 (154)
T TIGR01021 1 ELEERLIAVNRVSKVVKGGRRFSFSALVVVGDGKGRVGFGFGKAKEVPDAIKKAVEKARKNLINVPLT-------KG-TI 72 (154)
T ss_pred CceeEEEEEeeeeEEecCCcEEEEEEEEEEECCCCeEeeeeeecchHHHHHHHHHHHHHhCeEEEecC-------CC-cc
Confidence 58999999999999999999999999999999999999999999999999999999999999999994 34 99
Q ss_pred eeeeeee-e---EEEeecCCCcceeeChhhHHhhcccC
Q psy4335 118 PCKRLTH-G---DQQIPGGRKSKVLSSPENLKVTSTSK 151 (152)
Q Consensus 118 ~~~v~gk-g---V~l~Pap~GtGiva~~~~k~il~lAg 151 (152)
||++.|| | |+|+|||+|+||+|++.+++||++||
T Consensus 73 ~~~v~gk~gs~~V~l~Pap~G~Gi~a~~~~~~il~laG 110 (154)
T TIGR01021 73 PHEVIGVSGAAKVLLKPASPGTGVIAGGAVRAILELAG 110 (154)
T ss_pred ceEEEEEECcEEEEEEECCCCCceEeCcHHHHHHHHcC
Confidence 9999999 6 99999999999999999999999998
No 8
>PRK00550 rpsE 30S ribosomal protein S5; Validated
Probab=100.00 E-value=6.2e-39 Score=252.46 Aligned_cols=107 Identities=28% Similarity=0.398 Sum_probs=104.2
Q ss_pred CCccceeEEEeeeeeeecCCeeEEEEEEEEecCCCceEEeeeecchhHHHHHHHHHHHHhhcceeeeecccCCcCCCCce
Q psy4335 37 SSLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVRRGYWGNKIGKPHT 116 (152)
Q Consensus 37 ~~l~~~vl~i~rV~k~tk~Gr~~rf~alVvvGn~nG~vG~G~gks~ev~~Ai~kA~~~Ak~nli~v~rgy~~~~~~~~hT 116 (152)
.+|+|+||+++||||||++||++||+|+|+|||+||++|||+||++|+++||++|+..|++||++|+|+ +||
T Consensus 11 ~~l~~~vl~v~rv~k~tk~Gr~~~f~alvvvGn~~G~vG~G~gKa~ev~~Ai~kA~~~A~~nl~~V~~~--------~~T 82 (168)
T PRK00550 11 LELEEKVVAINRVTKVVKGGRRFSFSALVVVGDGKGRVGFGYGKAREVPEAIRKAVEDAKKNMIKVPLV--------GGT 82 (168)
T ss_pred CCceEEEEEEeeeEEEecCCcEEEEEEEEEEECCCCeEeeeeeecchHHHHHHHHHHHHHhCEEEEecC--------CCc
Confidence 489999999999999999999999999999999999999999999999999999999999999999993 499
Q ss_pred eeeeeeee-e---EEEeecCCCcceeeChhhHHhhcccC
Q psy4335 117 VPCKRLTH-G---DQQIPGGRKSKVLSSPENLKVTSTSK 151 (152)
Q Consensus 117 I~~~v~gk-g---V~l~Pap~GtGiva~~~~k~il~lAg 151 (152)
|||++.|| + |+|+|||+|+||+|++.+++||++||
T Consensus 83 i~~~v~gk~gs~kV~l~Pap~G~Gl~a~~~i~~il~laG 121 (168)
T PRK00550 83 IPHEVIGKFGAAKVLLKPASEGTGVIAGGAVRAVLELAG 121 (168)
T ss_pred cceeEEEEEceEEEEEEeCCCCCceEeChHHHHHHHHcC
Confidence 99999999 6 99999999999999999999999998
No 9
>PF00333 Ribosomal_S5: Ribosomal protein S5, N-terminal domain; InterPro: IPR013810 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 S5 is one of the proteins from the small ribosomal subunit, and is a protein of 166 to 254 amino-acid residues. In Escherichia coli, S5 is known to be important in the assembly and function of the 30S ribosomal subunit. Mutations in S5 have been shown to increase translational error frequencies. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups bacterial, cyanelle, red algal chloroplast, archaeal and fungal mitochondrial S5; mammalian, Caenorhabditis elegans, Drosophila and plant S2; and yeast S4 (SUP44). This entry represents the N-terminal domain of ribosomal protein S5, which has an alpha-beta(3)-alpha structure that folds into two layers, alpha/beta.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZKQ_e 2XZN_E 2XZM_E 3O30_B 1S1H_E 3IZB_E 3U5C_C 3U5G_C 3O2Z_B 3BBN_E ....
Probab=99.94 E-value=1e-26 Score=158.53 Aligned_cols=67 Identities=40% Similarity=0.601 Sum_probs=64.8
Q ss_pred CccceeEEEeeeeeeecCCeeEEEEEEEEecCCCceEEeeeecchhHHHHHHHHHHHHhhcceeeee
Q psy4335 38 SLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVRR 104 (152)
Q Consensus 38 ~l~~~vl~i~rV~k~tk~Gr~~rf~alVvvGn~nG~vG~G~gks~ev~~Ai~kA~~~Ak~nli~v~r 104 (152)
+|++++|+++||++||++||++||+|||++||+||++|||+|||.|+++|+++|..+|++||++|+|
T Consensus 1 ~l~~~vl~v~rv~k~tk~Gr~~~~~alvvvGn~~G~vG~G~gKa~~~~~Ai~kA~~~A~knl~~V~R 67 (67)
T PF00333_consen 1 DLEEKVLEVKRVSKMTKGGRIFSFRALVVVGNGNGLVGFGVGKAKEVPDAIRKAKRKAKKNLIYVPR 67 (67)
T ss_dssp SHEEEEEEEEEEEEEETTEEEEEEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHHHCSEEE-SC
T ss_pred CceEEEEEEEEEEEEecCCceeEEEEEEEEecCCCcEecCcccchhHHHHHHHHHHHHHhCCEECcC
Confidence 5899999999999999999999999999999999999999999999999999999999999999987
No 10
>KOG2646|consensus
Probab=99.84 E-value=5.2e-22 Score=171.04 Aligned_cols=107 Identities=21% Similarity=0.215 Sum_probs=98.7
Q ss_pred CccceeEEE--eeeeeeecCCeeEEEEEEEEecCCCceEEeeeecch-hHHHHHHHHHHHHhhcceeeeecccCCcCCCC
Q psy4335 38 SLKDEVLKI--MPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSK-EVATAIRGAIILAKLSVVPVRRGYWGNKIGKP 114 (152)
Q Consensus 38 ~l~~~vl~i--~rV~k~tk~Gr~~rf~alVvvGn~nG~vG~G~gks~-ev~~Ai~kA~~~Ak~nli~v~rgy~~~~~~~~ 114 (152)
+|+.+.+.+ +++..||+.|+..+|+|||+|||+||.+|||+||+. +...|+.+|+..|.+||.+|+| | +.
T Consensus 181 Dfe~r~l~lvrr~~~~~~r~Gki~s~~~LVvvGn~nGaaG~~eGKa~~~~s~A~~ka~~rAv~~l~~ieR-y------E~ 253 (396)
T KOG2646|consen 181 DFELRHLELVRRRVENQNRKGKIASMYALVVVGNGNGAAGLGEGKAADPNSPAIYKAIGRAVRNLGYIER-Y------ER 253 (396)
T ss_pred hhhHHHHHHHHhhhhccccccceeeEEEEEEEecCCcceeeccccCcCccCHHHHHHHHHHHhhcCcccc-c------cC
Confidence 466777776 668888899999999999999999999999999999 7899999999999999999999 7 45
Q ss_pred ceeeeeeeee--e--EEEeecCCCcceeeChhhHHhhcccC
Q psy4335 115 HTVPCKRLTH--G--DQQIPGGRKSKVLSSPENLKVTSTSK 151 (152)
Q Consensus 115 hTI~~~v~gk--g--V~l~Pap~GtGiva~~~~k~il~lAg 151 (152)
|||++|+.-+ + ++|+.+|+|+|+.|||++.+||++||
T Consensus 254 rTiygDi~~r~~~~~l~mk~rp~GfGLrcn~il~kIC~~~G 294 (396)
T KOG2646|consen 254 RTIYGDIDDRFHEVRLDMKSRPDGFGLRCNPILIKICECAG 294 (396)
T ss_pred ccccccchhhhhhhhhhhhhCCCcccccccHHHHHHHHHhc
Confidence 9999999777 3 99999999999999999999999998
No 11
>PF03719 Ribosomal_S5_C: Ribosomal protein S5, C-terminal domain; InterPro: IPR005324 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 [, ]. This is a family of proteins related to the 30S ribosomal protein S5P from Sulfolobus acidocaldarius (O05641 from SWISSPROT). Ribosomal protein S5 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S5 is known to be important in the assembly and function of the 30S ribosomal subunit. Mutations in S5 have been shown to increase translational error frequencies.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZN_E 2XZM_E 2WDK_E 3KNJ_E 3HUY_E 2B9M_E 2Y18_E 1XMQ_E 1IBM_E 3TVF_H ....
Probab=98.72 E-value=9.8e-09 Score=71.10 Aligned_cols=31 Identities=6% Similarity=-0.020 Sum_probs=28.5
Q ss_pred eeee-e---EEEeecCCCcceeeChhhHHhhcccC
Q psy4335 121 RLTH-G---DQQIPGGRKSKVLSSPENLKVTSTSK 151 (152)
Q Consensus 121 v~gk-g---V~l~Pap~GtGiva~~~~k~il~lAg 151 (152)
++|| + |+|+|||+|+||+|++.++.||+|||
T Consensus 1 V~gk~g~~~V~l~Pap~G~Gl~a~~~vr~il~laG 35 (74)
T PF03719_consen 1 VTGKFGATKVFLKPAPPGTGLVAGGAVRAILELAG 35 (74)
T ss_dssp EEEEETTEEEEEEESCTTSCEESSHHHHHHHHHTT
T ss_pred CEEEEeeEEEEEEeCCCCcceeechhHHHHHHhcc
Confidence 4567 4 99999999999999999999999998
No 12
>smart00358 DSRM Double-stranded RNA binding motif.
Probab=65.66 E-value=26 Score=21.68 Aligned_cols=39 Identities=31% Similarity=0.289 Sum_probs=24.7
Q ss_pred eeEEEEEEEEecCCCceEEeeeecchhHHHHHHHHHHHHhhcc
Q psy4335 57 QRTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKLSV 99 (152)
Q Consensus 57 r~~rf~alVvvGn~nG~vG~G~gks~ev~~Ai~kA~~~Ak~nl 99 (152)
....|.+-|.+++. .++-|.|.++ .+|-+.|-..|...|
T Consensus 28 ~~~~f~~~v~i~~~--~~~~g~g~sK--k~Ak~~AA~~al~~L 66 (67)
T smart00358 28 HAPRFTVTVKVGGE--YTGEGEGSSK--KEAKQRAAEAALRSL 66 (67)
T ss_pred CCCcEEEEEEECCE--EEEEeccCCH--HHHHHHHHHHHHHhc
Confidence 34578888888653 5666666655 456667766665543
No 13
>cd00048 DSRM Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases.
Probab=61.03 E-value=36 Score=20.89 Aligned_cols=38 Identities=29% Similarity=0.271 Sum_probs=24.6
Q ss_pred CeeEEEEEEEEecCCCceEEeeeecchhHHHHHHHHHHHHhh
Q psy4335 56 GQRTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKL 97 (152)
Q Consensus 56 Gr~~rf~alVvvGn~nG~vG~G~gks~ev~~Ai~kA~~~Ak~ 97 (152)
+....|.+-|.+++ -..+.|.|+++. +|-+.|-..|..
T Consensus 29 ~~~~~f~~~v~i~~--~~~~~g~g~sKk--~Ak~~AA~~al~ 66 (68)
T cd00048 29 DHAPRFTVEVTVGG--KITGEGEGSSKK--EAKQNAAEAALR 66 (68)
T ss_pred CCCCeEEEEEEECC--EEEEEeecCCHH--HHHHHHHHHHHH
Confidence 33568888888866 367777776554 566666555543
No 14
>PF02294 7kD_DNA_binding: 7kD DNA-binding domain; InterPro: IPR003212 This family contains members of the hyperthermophilic archaebacterium 7kDa DNA-binding/endoribonuclease P2 family. There are five 7kDa DNA-binding proteins, 7a-7e, found as monomers in the cell. Protein 7e shows the tightest DNA-binding ability.; GO: 0003677 DNA binding, 0004521 endoribonuclease activity; PDB: 1SSO_A 2CVR_A 1B4O_A 2XIW_B 1WTV_A 1WTQ_A 1BF4_A 1WVL_B 1WTR_A 1WTP_B ....
Probab=54.01 E-value=25 Score=23.14 Aligned_cols=43 Identities=26% Similarity=0.450 Sum_probs=33.3
Q ss_pred cceeEEEeeeeeeecCCeeEEEEEEEEecCCCceEEeeeecchhHHH
Q psy4335 40 KDEVLKIMPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSKEVAT 86 (152)
Q Consensus 40 ~~~vl~i~rV~k~tk~Gr~~rf~alVvvGn~nG~vG~G~gks~ev~~ 86 (152)
+|+-+++..+.|+.+-|+..||.. -|+||.-|-|--.-++.+.
T Consensus 10 eekevdiskikkvwrvgkmvsfty----ddgngktgrgavsekdapk 52 (62)
T PF02294_consen 10 EEKEVDISKIKKVWRVGKMVSFTY----DDGNGKTGRGAVSEKDAPK 52 (62)
T ss_dssp EEEEEEGGGEEEEEECSSEEEEEE----ECSSSSEEEEEEECCCSSH
T ss_pred ccceecHHHHHHHHhhcceEEEEE----ecCCCcccccccccccChH
Confidence 466677888889999999999975 6889998888766655443
No 15
>PF12327 FtsZ_C: FtsZ family, C-terminal domain; InterPro: IPR024757 The FtsZ family of proteins are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ is a GTPase, like tubulin []. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea []. This entry represents a domain of FtsZ. In most FtsZ proteins is found in the C terminus, except in some alphaproteobacteria proteins where there is an extension C-terminal domain TIGR03483 from TIGRFAMs.; PDB: 2RHO_B 2RHJ_A 2VXY_A 2RHL_B 2RHH_A 2VAM_A 1W5F_B 2R75_1 2R6R_1 1RQ7_A ....
Probab=33.37 E-value=50 Score=23.27 Aligned_cols=24 Identities=21% Similarity=0.349 Sum_probs=17.2
Q ss_pred ceEEeeeecchh-HHHHHHHHHHHH
Q psy4335 72 GHIGLGVKCSKE-VATAIRGAIILA 95 (152)
Q Consensus 72 G~vG~G~gks~e-v~~Ai~kA~~~A 95 (152)
-++|+|.+++.+ +.+|+++|+...
T Consensus 3 A~iGiG~a~G~~r~~~Av~~Al~sp 27 (95)
T PF12327_consen 3 AMIGIGEASGENRAEEAVEQALNSP 27 (95)
T ss_dssp EEEEEEEEESTTHHHHHHHHHHTST
T ss_pred EEEEEEEECCccHHHHHHHHHHhCc
Confidence 368899988876 667777776544
No 16
>COG3360 Uncharacterized conserved protein [Function unknown]
Probab=29.89 E-value=53 Score=22.65 Aligned_cols=23 Identities=26% Similarity=0.195 Sum_probs=17.4
Q ss_pred cchh-HHHHHHHHHHHHhhcceee
Q psy4335 80 CSKE-VATAIRGAIILAKLSVVPV 102 (152)
Q Consensus 80 ks~e-v~~Ai~kA~~~Ak~nli~v 102 (152)
.|++ ...||+.|+.+|...+..+
T Consensus 14 tSp~S~d~Ai~~Ai~RA~~t~~~l 37 (71)
T COG3360 14 TSPTSIDAAIANAIARAADTLDNL 37 (71)
T ss_pred cCCccHHHHHHHHHHHHHhhhhcc
Confidence 3444 7889999999998766544
No 17
>PRK13187 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed
Probab=29.20 E-value=75 Score=27.57 Aligned_cols=14 Identities=7% Similarity=0.202 Sum_probs=12.5
Q ss_pred EEEeecCCCc---ceee
Q psy4335 126 DQQIPGGRKS---KVLS 139 (152)
Q Consensus 126 V~l~Pap~Gt---Giva 139 (152)
+.++|||.++ ||+=
T Consensus 33 vtl~PA~~~t~~~GIvF 49 (304)
T PRK13187 33 VRILPARPEDGVTGIVF 49 (304)
T ss_pred EEEEcCCCCCCCccEEE
Confidence 8999999999 9764
No 18
>PF10957 DUF2758: Protein of unknown function (DUF2758); InterPro: IPR020296 Cse60 is expressed during sporulation in Bacillus subtilis. Transcription commences around 2h after the start of sporulation and had an absolute requirement for the transcription factor sigmaE. Maximal expression of cse60 further depended on the DNA-binding protein SpoIIID. Cse60 is an acidic product of only 60 residues, whose function is not known [].
Probab=29.02 E-value=1.3e+02 Score=20.04 Aligned_cols=39 Identities=23% Similarity=0.218 Sum_probs=26.7
Q ss_pred chhhhhcccCCCccceeEEEeeeeeeec---CCeeEEEEEEEE
Q psy4335 27 EFEIIDFFIGSSLKDEVLKIMPVQKQTR---AGQRTRFKAFVA 66 (152)
Q Consensus 27 e~eiid~~~~~~l~~~vl~i~rV~k~tk---~Gr~~rf~alVv 66 (152)
|.+|=+||- ..=++++++|+-...++. +-+.+.|+||++
T Consensus 16 e~~vN~fL~-~~~~~~viDIKy~va~~~~~~~eq~y~fSamIi 57 (60)
T PF10957_consen 16 EDQVNDFLA-KLDDDQVIDIKYQVAASCDDEDEQIYCFSAMII 57 (60)
T ss_pred HHHHHHHHH-hCCCCcEEEEEEEEEEeccCCcceeEEEEEEEE
Confidence 455556663 234568999988766663 356779999987
No 19
>PRK13186 lpxC UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed
Probab=28.28 E-value=39 Score=29.14 Aligned_cols=14 Identities=7% Similarity=0.031 Sum_probs=12.3
Q ss_pred EEEeecCCCcceee
Q psy4335 126 DQQIPGGRKSKVLS 139 (152)
Q Consensus 126 V~l~Pap~GtGiva 139 (152)
+.++|||.++||+=
T Consensus 26 v~~~PA~~~tGI~F 39 (295)
T PRK13186 26 LTLRPAPANTGIVF 39 (295)
T ss_pred EEEEcCCCCCEEEE
Confidence 78999999999763
No 20
>PF07311 Dodecin: Dodecin; InterPro: IPR009923 This entry represents proteins with a Dodecin-like topology. Dodecin flavoprotein is a small dodecameric flavin-binding protein from Halobacterium salinarium (Halobacterium halobium) that contains two flavins stacked in a single binding pocket between two tryptophan residues to form an aromatic tetrade []. Dodecin binds riboflavin, although it appears to have a broad specificity for flavins. Lumichrome, a molecule associated with flavin metabolism, appears to be a ligand of dodecin, which could act as a waste-trapping device. ; PDB: 2VYX_L 2DEG_F 2V18_K 2V19_D 2UX9_B 2CZ8_E 2V21_F 2CC8_A 2CCB_A 2VX9_A ....
Probab=27.17 E-value=68 Score=21.70 Aligned_cols=22 Identities=23% Similarity=0.294 Sum_probs=17.0
Q ss_pred hhHHHHHHHHHHHHhhcceeee
Q psy4335 82 KEVATAIRGAIILAKLSVVPVR 103 (152)
Q Consensus 82 ~ev~~Ai~kA~~~Ak~nli~v~ 103 (152)
....+|++.|+..|.+.+--++
T Consensus 14 ~S~edAv~~Av~~A~kTl~ni~ 35 (66)
T PF07311_consen 14 KSWEDAVQNAVARASKTLRNIR 35 (66)
T ss_dssp SHHHHHHHHHHHHHHHHSSSEE
T ss_pred CCHHHHHHHHHHHHhhchhCcE
Confidence 4578999999999987665443
No 21
>PF04098 Rad52_Rad22: Rad52/22 family double-strand break repair protein; InterPro: IPR007232 The DNA single-strand annealing proteins (SSAPs), such as RecT, Red-beta, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. This family includes proteins related to Rad52. These proteins contain two helix-hairpin-helix motifs [].; GO: 0006281 DNA repair, 0006310 DNA recombination; PDB: 1KN0_I 1H2I_U.
Probab=27.16 E-value=2.8e+02 Score=21.05 Aligned_cols=66 Identities=17% Similarity=0.297 Sum_probs=31.1
Q ss_pred hcccC-CCccceeEEEee-eeeeecC-CeeE--EEE--EEEEecCCCce--EEeeeecc-hh----HHHHHHHHHHHHhh
Q psy4335 32 DFFIG-SSLKDEVLKIMP-VQKQTRA-GQRT--RFK--AFVAIGDSNGH--IGLGVKCS-KE----VATAIRGAIILAKL 97 (152)
Q Consensus 32 d~~~~-~~l~~~vl~i~r-V~k~tk~-Gr~~--rf~--alVvvGn~nG~--vG~G~gks-~e----v~~Ai~kA~~~Ak~ 97 (152)
|-.+| ..|..+++.+.. ....... | +. .+. +=+.+-|+.-+ +|+|.... .. ...|.+.|+.+|.+
T Consensus 43 N~vfGfngWs~~i~~~~~~~~~~~~~~~-~~~~~~~~~vritLkdg~~~e~~G~g~~~~~~~k~~a~~~akK~AvtdAlK 121 (154)
T PF04098_consen 43 NEVFGFNGWSSEIISLEQDFVEEEPGEG-KYSVGYSAIVRITLKDGTYREDIGYGWSENMDGKGMAIEKAKKGAVTDALK 121 (154)
T ss_dssp HHHH-TTTEEEEEEEEEEEEEEESSS---SEEEEEEEEEEEEETTS-EEEEEEEEEEESES-HHHHHHHHHHHHHHHHHH
T ss_pred HHHhCcCCCceEEEeeEeeeeeccCCce-eEEEEEEEEEEEEEeCCceeeecceEEEecCCccchhhhhhHHHHHHHHHH
Confidence 33445 478888888877 2232222 2 22 222 23344555533 55555542 11 34455555555554
Q ss_pred c
Q psy4335 98 S 98 (152)
Q Consensus 98 n 98 (152)
+
T Consensus 122 R 122 (154)
T PF04098_consen 122 R 122 (154)
T ss_dssp H
T ss_pred H
Confidence 3
No 22
>TIGR00325 lpxC UDP-3-0-acyl N-acetylglucosamine deacetylase. UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc deacetylase from E. coli, LpxC, was previously designated EnvA. This enzyme is involved in lipid-A precursor biosynthesis. It is essential for cell viability.
Probab=26.63 E-value=43 Score=28.92 Aligned_cols=14 Identities=14% Similarity=0.088 Sum_probs=12.2
Q ss_pred EEEeecCCCcceee
Q psy4335 126 DQQIPGGRKSKVLS 139 (152)
Q Consensus 126 V~l~Pap~GtGiva 139 (152)
+.++|||.++||+=
T Consensus 25 ltl~PA~~~tGI~F 38 (297)
T TIGR00325 25 LTLRPAAANTGVVF 38 (297)
T ss_pred EEEEcCCCCCcEEE
Confidence 78899999999764
No 23
>KOG3438|consensus
Probab=26.41 E-value=36 Score=25.18 Aligned_cols=30 Identities=10% Similarity=-0.162 Sum_probs=22.4
Q ss_pred ceeeeeeeee-eEEEeecCCCcceeeChhhHHhh
Q psy4335 115 HTVPCKRLTH-GDQQIPGGRKSKVLSSPENLKVT 147 (152)
Q Consensus 115 hTI~~~v~gk-gV~l~Pap~GtGiva~~~~k~il 147 (152)
+||||+..-+ ++++..++ |+.|-++.++=|
T Consensus 48 YtIPHPse~k~niRIQt~~---~~~A~evl~kgl 78 (105)
T KOG3438|consen 48 YTIPHPSEDKINIRIQTRD---GDPAVEVLKKGL 78 (105)
T ss_pred ccCCCCchhhheEEEEecC---CCcchHHHHHHH
Confidence 6999999999 76665554 567777777654
No 24
>PRK15184 curli production assembly/transport protein CsgG; Provisional
Probab=25.58 E-value=1.2e+02 Score=26.00 Aligned_cols=65 Identities=17% Similarity=0.212 Sum_probs=39.4
Q ss_pred eEEEeeeeeeecCCeeEEEEEEEEecC-CCceEEeeeecchhHHHHHHHHHHHHhhcce--eeeecccC
Q psy4335 43 VLKIMPVQKQTRAGQRTRFKAFVAIGD-SNGHIGLGVKCSKEVATAIRGAIILAKLSVV--PVRRGYWG 108 (152)
Q Consensus 43 vl~i~rV~k~tk~Gr~~rf~alVvvGn-~nG~vG~G~gks~ev~~Ai~kA~~~Ak~nli--~v~rgy~~ 108 (152)
|+..-.++|++- |+-.+-.+|-.++. .=--++.|...-.-+.-|++.||.+|...|+ -+++++|.
T Consensus 186 Vl~sVt~sKtI~-s~~i~AG~Frfv~~~~lle~e~G~t~nEP~qlaVr~aIE~AV~~li~~g~~~~~w~ 253 (277)
T PRK15184 186 ILSSVNTSKTIL-SYEVQAGVFRFIDYQRLLEGEVGYTSNEPVMLCLMSAIETGVIFLINDGIDRGLWD 253 (277)
T ss_pred EEEEEEEEEEEE-EeeeccceEEEeccceeEEeecCcccCChHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 344444555443 23333333444442 2333555655555588899999999999988 47888995
No 25
>PF02624 YcaO: YcaO-like family; InterPro: IPR003776 This domain comprises the whole of a protein in Methanocaldococcus jannaschii (Methanococcus jannaschii) and Methanobacterium thermoautotrophicum, all but the N-terminal 60 residues from a protein of Mycobacterium tuberculosis, and all but the C-terminal 180 residues from a protein in Haemophilus influenzae and Escherichia coli, among proteins from published complete genomes.
Probab=25.47 E-value=1.3e+02 Score=24.83 Aligned_cols=35 Identities=14% Similarity=0.078 Sum_probs=28.7
Q ss_pred CCCceEEeeeecchhHHHHHHHHHHHHhhcceeee
Q psy4335 69 DSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVR 103 (152)
Q Consensus 69 n~nG~vG~G~gks~ev~~Ai~kA~~~Ak~nli~v~ 103 (152)
+..+..-+|.|++.+...|+.+|+.-|........
T Consensus 198 ~~~~~~~~G~ga~~~~~~Al~rAl~E~~q~~~~~~ 232 (332)
T PF02624_consen 198 KDRPYYAVGAGAHLDPEEALERALTEAAQSRLLFI 232 (332)
T ss_pred CCCcceEEEeccCCCHHHHHHHHHHHHHHHHHHHH
Confidence 55777899999999999999999999876654433
No 26
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=25.21 E-value=3.3e+02 Score=22.06 Aligned_cols=37 Identities=19% Similarity=0.196 Sum_probs=24.5
Q ss_pred CeeEEEEEEEEecCCCceEEeeeecchhHHHHHHHHHHHHh
Q psy4335 56 GQRTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAK 96 (152)
Q Consensus 56 Gr~~rf~alVvvGn~nG~vG~G~gks~ev~~Ai~kA~~~Ak 96 (152)
.....|.+-|.+++ ...|-|.|+|+. .|=+.|-..|-
T Consensus 136 dH~~~Ftv~V~V~g--~~~g~G~G~SKK--eAEQ~AAk~AL 172 (183)
T PHA02701 136 DHCPLFTCTIVVSG--KVVATASGCSKK--LARHAACADAL 172 (183)
T ss_pred CCCceEEEEEEECC--EEEEEEEeCCHH--HHHHHHHHHHH
Confidence 56678999999975 457777777774 44444444443
No 27
>PRK00102 rnc ribonuclease III; Reviewed
Probab=24.82 E-value=2.1e+02 Score=22.51 Aligned_cols=38 Identities=24% Similarity=0.240 Sum_probs=25.5
Q ss_pred eEEEEEEEEecCCCceEEeeeecchhHHHHHHHHHHHHhhcc
Q psy4335 58 RTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKLSV 99 (152)
Q Consensus 58 ~~rf~alVvvGn~nG~vG~G~gks~ev~~Ai~kA~~~Ak~nl 99 (152)
...|.+-|.+++ -.+|.|.|+++ ..|-+.|...|..+|
T Consensus 189 ~~~f~~~v~i~~--~~~~~g~g~sk--k~Ae~~AA~~Al~~l 226 (229)
T PRK00102 189 DKEFTVEVTVNG--KELGEGTGSSK--KEAEQAAAKQALKKL 226 (229)
T ss_pred CceEEEEEEECC--EEEEEeeeCCH--HHHHHHHHHHHHHHH
Confidence 356777778764 35777776655 477777777776654
No 28
>COG1153 FwdD Formylmethanofuran dehydrogenase subunit D [Energy production and conversion]
Probab=24.79 E-value=50 Score=25.21 Aligned_cols=35 Identities=23% Similarity=0.292 Sum_probs=25.1
Q ss_pred cceeeeecccCCcCCCCceeeeeeeee-e--EEEeecC
Q psy4335 98 SVVPVRRGYWGNKIGKPHTVPCKRLTH-G--DQQIPGG 132 (152)
Q Consensus 98 nli~v~rgy~~~~~~~~hTI~~~v~gk-g--V~l~Pap 132 (152)
+++++++|.|.|..-+|.|-.+-.-+= | |.+.|+-
T Consensus 73 G~vfiPmgpWaN~vi~P~T~sTG~P~fKgipv~ie~td 110 (128)
T COG1153 73 GMVFIPMGPWANVVIDPDTDSTGMPGFKGIPVEVEPTD 110 (128)
T ss_pred CeEEecCCcccceeeCCCCCCcCCcccCCceEEEEeCC
Confidence 689999999999887887743322222 3 8888875
No 29
>PF02482 Ribosomal_S30AE: Sigma 54 modulation protein / S30EA ribosomal protein; InterPro: IPR003489 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 [, ]. This family contains the sigma-54 modulation protein family and the S30Ae family of ribosomal proteins which includes the light-repressed protein (lrtA) [].; GO: 0005488 binding, 0044238 primary metabolic process; PDB: 1L4S_A 1VOX_a 1VOV_a 3V2E_Y 3V2C_Y 1N3G_A 1VOS_a 1VOZ_a 1VOQ_a 1IMU_A ....
Probab=24.38 E-value=2.3e+02 Score=19.03 Aligned_cols=29 Identities=17% Similarity=0.231 Sum_probs=24.2
Q ss_pred CceEEeeeecchhHHHHHHHHHHHHhhcc
Q psy4335 71 NGHIGLGVKCSKEVATAIRGAIILAKLSV 99 (152)
Q Consensus 71 nG~vG~G~gks~ev~~Ai~kA~~~Ak~nl 99 (152)
.|..=.+...+.++-+||..|+....+.|
T Consensus 59 ~~~~l~a~~~~~d~~~Aid~a~dkl~rql 87 (97)
T PF02482_consen 59 PGHVLVAEESAEDLYAAIDEAFDKLERQL 87 (97)
T ss_dssp TTEEEEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred CCceEEEEEecCCHHHHHHHHHHHHHHHH
Confidence 56666788889999999999999887755
No 30
>KOG3769|consensus
Probab=23.03 E-value=22 Score=31.11 Aligned_cols=77 Identities=16% Similarity=0.173 Sum_probs=52.3
Q ss_pred HHhhcCCCCCchhhhhcccCCCccceeEEEeeeeeeecC-CeeEEEEEEEEecCCCceEEeeeecchhHHHHHHHHHHHH
Q psy4335 17 QIYLFSLPIKEFEIIDFFIGSSLKDEVLKIMPVQKQTRA-GQRTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILA 95 (152)
Q Consensus 17 ~~~~~~l~i~e~eiid~~~~~~l~~~vl~i~rV~k~tk~-Gr~~rf~alVvvGn~nG~vG~G~gks~ev~~Ai~kA~~~A 95 (152)
|+|.+-+|++ ++.+.+-..+++ ..+.+.++. |+.. --.+.+||=|-|.==+|.|-+.++..|-+.|-..|
T Consensus 227 ~m~ql~~P~~--~L~~lckr~~l~------epe~Rll~esGr~S-~~PvyvVgiYs~kkllGqG~Gesl~~A~e~AA~dA 297 (333)
T KOG3769|consen 227 EMWQLQWPRR--LLSRLCKRRGLK------EPESRLLAESGRNS-AEPVYVVGIYSGKKLLGQGQGESLKLAEEQAARDA 297 (333)
T ss_pred hhccccchHH--HHHHHHHHcCCC------CchhHHHHHhccCc-cCceEEEEeecCchhhccCcchHHHHHHHHHHHHH
Confidence 6666666654 223433223333 345566654 5554 45566779999988888888999999999999999
Q ss_pred hhcceee
Q psy4335 96 KLSVVPV 102 (152)
Q Consensus 96 k~nli~v 102 (152)
-..++-.
T Consensus 298 L~k~y~~ 304 (333)
T KOG3769|consen 298 LIKLYDH 304 (333)
T ss_pred HHHHHcC
Confidence 8877533
No 31
>PF08502 LeuA_dimer: LeuA allosteric (dimerisation) domain; InterPro: IPR013709 This is the C-terminal regulatory (R) domain of alpha-isopropylmalate synthase, which catalyses the first committed step in the leucine biosynthetic pathway []. This domain, is an internally duplicated structure with a novel fold []. It comprises two similar units that are arranged such that the two -helices pack together in the centre, crossing at an angle of 34 degrees, sandwiched between the two three-stranded, antiparallel beta-sheets. The overall domain is thus constructed as a beta-alpha-beta three-layer sandwich []. ; GO: 0003852 2-isopropylmalate synthase activity, 0009098 leucine biosynthetic process; PDB: 3HQ1_A 3HPZ_B 1SR9_A 3FIG_B 3HPS_A 3F6G_A 3F6H_A.
Probab=23.00 E-value=1.8e+02 Score=21.26 Aligned_cols=44 Identities=25% Similarity=0.330 Sum_probs=33.9
Q ss_pred CCeeEEEEEEEEecCCCceEEeeeecchhHHHHHHHHHHHHhhc
Q psy4335 55 AGQRTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKLS 98 (152)
Q Consensus 55 ~Gr~~rf~alVvvGn~nG~vG~G~gks~ev~~Ai~kA~~~Ak~n 98 (152)
.|.-.+-.+.|-+-+.+|..=+|+|.+.++..|--+|+..|..+
T Consensus 88 ~gsda~a~a~V~i~~~~g~~~~G~g~~~Di~~As~~A~~~AiNr 131 (133)
T PF08502_consen 88 SGSDAQAEAYVEIEDEDGRTVWGVGIDTDIVEASLKAYLSAINR 131 (133)
T ss_dssp TSTT-EEEEEEEEEE-GGGEEEEEEEESSHHHHHHHHHHHHHHH
T ss_pred CCCCcEEEEEEEEEECCCcEEEEEEECCCHHHHHHHHHHHHHHh
Confidence 45556677888888777888888888999999999999888654
No 32
>PF03331 LpxC: UDP-3-O-acyl N-acetylglycosamine deacetylase; InterPro: IPR004463 UDP-3-O-N-acetylglucosamine deacetylases are zinc-dependent metalloamidases that catalyse the second and committed step in the biosynthesis of lipid A. Lipid A anchors lipopolysaccharide (the major constituent of the outer membrane) into the membrane in Gram negative bacteria. LpxC shows no homology to mammalian metalloamidases and is essential for cell viability, making it an important target for the development of novel antibacterial compounds []. The structure of UDP-3-O-N-acetylglucosamine deacetylase (LpxC) from Aquifex aeolicus has a two-layer alpha/beta structure similar to that of the second domain of ribosomal protein S5, only in LpxC there is a duplication giving two structural repeats of this fold, each repeat being elaborated with additional structures forming the active site. LpxC contains a zinc-binding motif, which resides at the base of an active site cleft and adjacent to a hydrophobic tunnel occupied by a fatty acid []. This tunnel accounts for the specificity of LpxC toward substrates and inhibitors bearing appropriately positioned 3-O-fatty acid substituents []. This entry represents the UDP-3-O-N-acetylglucosamine deacetylase family of proteins.; GO: 0008759 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity, 0009245 lipid A biosynthetic process; PDB: 2VES_C 3U1Y_A 3P3E_A 3UHM_A 1XXE_A 2IER_A 1YH8_B 2GO4_A 2O3Z_B 2GO3_B ....
Probab=22.75 E-value=55 Score=27.94 Aligned_cols=13 Identities=8% Similarity=0.105 Sum_probs=8.8
Q ss_pred EEEeecCCCccee
Q psy4335 126 DQQIPGGRKSKVL 138 (152)
Q Consensus 126 V~l~Pap~GtGiv 138 (152)
+.+.|||.++|++
T Consensus 25 l~l~PA~~~~Gi~ 37 (277)
T PF03331_consen 25 LTLRPAPANTGIV 37 (277)
T ss_dssp EEEEE--TT-EEE
T ss_pred EEEEECCCCCCEE
Confidence 7889999999986
No 33
>PF09843 DUF2070: Predicted membrane protein (DUF2070); InterPro: IPR019204 This domain of unknown function is found in various bacterial and archael hypothetical proteins, as well as in prokaryotic polyketide synthase.
Probab=22.68 E-value=1.9e+02 Score=22.57 Aligned_cols=46 Identities=24% Similarity=0.283 Sum_probs=34.0
Q ss_pred EEEEEEEecCCCceEEeeeecchhHHHHHHHHHHHHhhcceeeeecc
Q psy4335 60 RFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVRRGY 106 (152)
Q Consensus 60 rf~alVvvGn~nG~vG~G~gks~ev~~Ai~kA~~~Ak~nli~v~rgy 106 (152)
.|.-.+..|++--.+|.-+ ...++...++.+...|..++-+++-+|
T Consensus 112 H~~~~~~~g~~y~~vG~~~-~~~~i~~~~~~~~~~A~~~l~~v~~~~ 157 (179)
T PF09843_consen 112 HFVNGESGGNGYWPVGPLI-PPREIIESRREAVSEAERDLEPVEVGY 157 (179)
T ss_pred cEEccEECCccceeccccC-CHHHHHHHHHHHHHHHHhcccccEEEE
Confidence 3444455555444566555 788899999999999999999998754
No 34
>PRK13188 bifunctional UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase/(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase; Reviewed
Probab=22.53 E-value=59 Score=29.77 Aligned_cols=17 Identities=6% Similarity=-0.230 Sum_probs=14.2
Q ss_pred ee-e-EEEeecCCCcceee
Q psy4335 123 TH-G-DQQIPGGRKSKVLS 139 (152)
Q Consensus 123 gk-g-V~l~Pap~GtGiva 139 (152)
|+ . +.++|||.++||+=
T Consensus 22 G~~~~~~~~Pa~~~~Gi~F 40 (464)
T PRK13188 22 GKEVTITFKPAPENHGYKF 40 (464)
T ss_pred CcEEEEEEEcCCCCCcEEE
Confidence 55 3 99999999999864
No 35
>cd03315 MLE_like Muconate lactonizing enzyme (MLE) like subgroup of the enolase superfamily. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and residues that can function as general acid/base catalysts, a Lys-X-Lys motif and another conserved lysine. Despite these conserved residues, the members of the MLE subgroup, like muconate lactonizing enzyme, o-succinylbenzoate synthase (OSBS) and N-acylamino acid racemase (NAAAR), catalyze different reactions.
Probab=22.00 E-value=1.8e+02 Score=23.51 Aligned_cols=32 Identities=13% Similarity=0.122 Sum_probs=23.8
Q ss_pred EEEEEEecCCCceEEeeeecchhHHHHHHHHHHHHh
Q psy4335 61 FKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAK 96 (152)
Q Consensus 61 f~alVvvGn~nG~vG~G~gks~ev~~Ai~kA~~~Ak 96 (152)
-..+|-+-+.+|.+|+|... ..||+-|..++.
T Consensus 25 ~~~~v~l~~~~G~~G~GE~~----~~aid~Al~Dl~ 56 (265)
T cd03315 25 DHVLLRLHTDDGLVGWAEAT----KAAVDMALWDLW 56 (265)
T ss_pred ceEEEEEEECCCCEEEeccH----HHHHHHHHHHHH
Confidence 34666676678999999754 678888888654
No 36
>PF13867 SAP30_Sin3_bdg: Sin3 binding region of histone deacetylase complex subunit SAP30; PDB: 2LD7_A.
Probab=21.89 E-value=27 Score=22.30 Aligned_cols=14 Identities=43% Similarity=0.700 Sum_probs=8.4
Q ss_pred CCCCCchhhhhccc
Q psy4335 22 SLPIKEFEIIDFFI 35 (152)
Q Consensus 22 ~l~i~e~eiid~~~ 35 (152)
++||.|.|+|-.|+
T Consensus 36 s~~v~E~evI~~Fl 49 (53)
T PF13867_consen 36 SQPVDENEVIANFL 49 (53)
T ss_dssp T----HHHHHHHHH
T ss_pred cCCCCHHHHHHHHH
Confidence 89999999987765
No 37
>TIGR02191 RNaseIII ribonuclease III, bacterial. This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family.
Probab=20.61 E-value=3.3e+02 Score=21.20 Aligned_cols=37 Identities=24% Similarity=0.148 Sum_probs=25.0
Q ss_pred eEEEEEEEEecCCCceEEeeeecchhHHHHHHHHHHHHhhc
Q psy4335 58 RTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKLS 98 (152)
Q Consensus 58 ~~rf~alVvvGn~nG~vG~G~gks~ev~~Ai~kA~~~Ak~n 98 (152)
...|.+-|.+++ -.+|-|.|+++ ..|-+.|...|...
T Consensus 183 ~~~f~~~v~~~~--~~~~~g~g~sk--k~A~~~AA~~Al~~ 219 (220)
T TIGR02191 183 DKEFTVEVSVNG--EPYGEGKGKSK--KEAEQNAAKAALEK 219 (220)
T ss_pred CceEEEEEEECC--EEEEEeeeCCH--HHHHHHHHHHHHHh
Confidence 347777777763 45666666654 67777887777654
Done!