Query 021869
Match_columns 306
No_of_seqs 183 out of 1108
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 06:17:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021869.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021869hhsearch_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 2.4E-58 5.3E-63 426.4 16.0 180 112-291 34-229 (257)
2 TIGR01020 rpsE_arch ribosomal 100.0 6.3E-58 1.4E-62 415.2 16.3 177 112-288 5-198 (212)
3 PRK04044 rps5p 30S ribosomal p 100.0 1.6E-57 3.4E-62 412.7 18.8 187 112-298 6-211 (211)
4 COG0098 RpsE Ribosomal protein 100.0 5.7E-57 1.2E-61 399.5 17.7 160 146-305 20-179 (181)
5 PRK00550 rpsE 30S ribosomal pr 100.0 2.3E-56 4.9E-61 393.4 19.4 158 147-305 10-167 (168)
6 TIGR01021 rpsE_bact ribosomal 100.0 6.5E-56 1.4E-60 385.8 19.5 154 149-303 1-154 (154)
7 KOG0877 40S ribosomal protein 100.0 7.9E-49 1.7E-53 352.1 11.0 190 112-303 6-210 (213)
8 CHL00138 rps5 ribosomal protei 100.0 1.2E-44 2.6E-49 311.9 15.6 122 148-269 22-143 (143)
9 KOG2646 Ribosomal protein S5 [ 100.0 3.7E-43 8E-48 337.2 7.2 206 90-305 127-340 (396)
10 PF03719 Ribosomal_S5_C: Ribos 99.9 6.9E-28 1.5E-32 187.0 10.0 74 225-298 1-74 (74)
11 PF00333 Ribosomal_S5: Ribosom 99.9 3.6E-24 7.8E-29 163.7 7.9 67 149-215 1-67 (67)
12 cd00048 DSRM Double-stranded R 54.7 48 0.001 23.1 5.7 39 167-209 29-67 (68)
13 smart00358 DSRM Double-strande 45.9 61 0.0013 22.7 5.1 40 167-210 27-66 (67)
14 PF14493 HTH_40: Helix-turn-he 44.3 28 0.0006 27.4 3.3 27 276-302 2-28 (91)
15 PF02624 YcaO: YcaO-like famil 44.0 20 0.00043 33.7 2.8 132 76-214 95-232 (332)
16 PF00035 dsrm: Double-stranded 43.2 1E+02 0.0022 21.8 5.9 43 164-210 25-67 (67)
17 cd01684 Tet_like_IV EF-G_domai 40.0 90 0.0019 25.6 5.8 18 229-246 25-42 (115)
18 COG1710 Uncharacterized protei 39.2 47 0.001 29.0 4.1 55 249-304 68-126 (139)
19 PF06207 DUF1002: Protein of u 34.9 64 0.0014 30.4 4.6 38 233-270 54-103 (225)
20 CHL00130 rbcS ribulose-1,5-bis 28.2 48 0.001 29.3 2.4 27 92-118 8-34 (138)
21 PLN02289 ribulose-bisphosphate 26.8 48 0.001 30.3 2.2 27 92-118 70-96 (176)
22 PRK12371 ribonuclease III; Rev 25.9 1.2E+02 0.0026 28.3 4.7 40 167-210 190-229 (235)
23 cd03527 RuBisCO_small Ribulose 25.2 61 0.0013 26.9 2.4 27 92-118 6-32 (99)
24 cd01434 EFG_mtEFG1_IV EFG_mtEF 24.7 2.1E+02 0.0046 23.1 5.6 21 226-246 22-42 (116)
25 PF02482 Ribosomal_S30AE: Sigm 23.8 1.1E+02 0.0025 23.5 3.6 42 166-210 46-87 (97)
26 PF13542 HTH_Tnp_ISL3: Helix-t 22.9 1.6E+02 0.0034 20.2 3.8 35 269-303 9-43 (52)
27 COG3360 Uncharacterized conser 22.6 1.5E+02 0.0032 23.5 3.9 23 194-216 18-40 (71)
28 PF04098 Rad52_Rad22: Rad52/22 22.2 4.7E+02 0.01 22.6 7.5 12 148-159 49-60 (154)
29 TIGR02191 RNaseIII ribonucleas 22.1 1.4E+02 0.0031 26.5 4.4 38 169-210 183-220 (220)
30 PRK13832 plasmid partitioning 21.4 2.6E+02 0.0056 29.7 6.6 69 236-304 46-135 (520)
31 cd07018 S49_SppA_67K_type Sign 21.2 4.6E+02 0.0099 23.8 7.6 125 170-304 45-187 (222)
32 PRK00102 rnc ribonuclease III; 20.8 1.9E+02 0.0042 25.9 5.0 38 169-210 189-226 (229)
33 PF12327 FtsZ_C: FtsZ family, 20.5 75 0.0016 25.5 2.0 21 184-204 4-25 (95)
34 cd00308 enolase_like Enolase-s 20.3 1.2E+02 0.0025 27.4 3.5 39 172-215 25-63 (229)
No 1
>PTZ00070 40S ribosomal protein S2; Provisional
Probab=100.00 E-value=2.4e-58 Score=426.45 Aligned_cols=180 Identities=31% Similarity=0.464 Sum_probs=172.2
Q ss_pred CCCcccccCCCCcccccchhhhhh-ccCC-CCccccccCCc------ceeEEEEeeeeeeecCCeeEEEEEEEEecCCCC
Q 021869 112 GPAYAGVSVLGNDVYVMDSKAKKT-SAFG-KTKKEKVKDGF------EERVVQVRRVTKVVKGGKQLKFRAIVVVGDKKG 183 (306)
Q Consensus 112 ~rgwsg~t~lG~~V~~~~~k~~~~-~~fs-~~ke~~i~d~f------~~~VL~i~rV~K~TkgGR~~rf~AlVvVGNgnG 183 (306)
+.+|.|.|+|||+|+++++++.++ |.|+ |++|.+|+|.| .++||+|+||||||++||++||+|||||||+||
T Consensus 34 ~~~W~P~TklGrlVk~gki~s~eei~~~~lpikE~eIvd~ll~~~~L~eeVl~I~rVqK~TkgGrr~rF~AlVVVGd~nG 113 (257)
T PTZ00070 34 EKEWVPVTKLGRLVKAGKITSLEEIFLFSIPIKEYQIVDHFFAESKLKDEVMKIMPVQKQTSAGQRTRFKAFVVVGDGNG 113 (257)
T ss_pred cCceeeccchhhhhhcCccccHHHHHhcCCCccchhhHHHHccCccchheEEEEeeeEEEecCCcEEEEEEEEEEeCCCC
Confidence 457999999999999999999988 9999 99999999766 479999999999999999999999999999999
Q ss_pred ceeecccchhhHHHHHHHHHHHHHhcceEeccc-------CCcccceeeeeeeceEEEEEeecCCCCceeechHHHHHHH
Q 021869 184 QVGVGVAKAKEVIAAVQKSAVDARRNIVTVPMT-------KYLTFPHRSDGDFGAAKVMLRPASPGTGVIAGGAVRIVLE 256 (306)
Q Consensus 184 ~vG~GvGKakev~~AIrKA~~~Ak~nLi~V~~~-------~~hTIphdv~gk~gstkV~L~PAP~GtGLva~~vik~Ile 256 (306)
+||+|+|||+||.+||+||+++|++||++|+++ ++|||||+|+|||||++|+|+|||+|+||+|++++++||+
T Consensus 114 ~VGlG~gKakEV~~AIrKAi~~AK~nii~V~rgyW~~~~g~~hTIp~~V~GK~GSv~V~L~PAP~GtGivAg~~vk~VLe 193 (257)
T PTZ00070 114 HIGLGAKVAKEVATAIRGAIIAAKLNLVPVRRGYWGNKIGEPHTVPMKVTGKCGSVRVRLVPAPRGTGIVAAPTPKKILE 193 (257)
T ss_pred cEecceeechhHHHHHHHHHHHHHhCeEEEecccccccCCCCCCeeeeEEEEeCeEEEEEEeCCCCccEEeCcHHHHHHH
Confidence 999999999999999999999999999999983 6799999999999999999999999999999999999999
Q ss_pred HhCccceeeeeccCC-chhhHHHHHHHHHHccCCHH
Q 021869 257 MAGVENALGKQLGSN-NALNNARATVVAVQKMKQWR 291 (306)
Q Consensus 257 lAGIkD~~aKv~GSt-n~lNvaKAtf~AL~k~~S~~ 291 (306)
||||+|||+|++||+ |++|++||||+||.++|++.
T Consensus 194 lAGIkDv~tks~GsTrt~~N~aKATf~AL~~t~~~~ 229 (257)
T PTZ00070 194 FAGVEDVFTSSRGKTRTRGNFLKATFYALRKTYGFL 229 (257)
T ss_pred HcCccceeeecccCCCChHHHHHHHHHHHHHHhccc
Confidence 999999999999987 78999999999999998754
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=6.3e-58 Score=415.16 Aligned_cols=177 Identities=32% Similarity=0.490 Sum_probs=171.1
Q ss_pred CCCcccccCCCCcccccchhhhhh-ccCC-CCccccccCCc-----ceeEEEEeeeeeeecCCeeEEEEEEEEecCCCCc
Q 021869 112 GPAYAGVSVLGNDVYVMDSKAKKT-SAFG-KTKKEKVKDGF-----EERVVQVRRVTKVVKGGKQLKFRAIVVVGDKKGQ 184 (306)
Q Consensus 112 ~rgwsg~t~lG~~V~~~~~k~~~~-~~fs-~~ke~~i~d~f-----~~~VL~i~rV~K~TkgGR~~rf~AlVvVGNgnG~ 184 (306)
+.+|.|.|+|||+|++.++++.++ +.|+ |++|.||.|.| +++||+|+||||||++||++||+|+|||||+||+
T Consensus 5 ~~~w~p~t~lgrlV~~g~i~s~~ei~~~~~~i~E~eivd~ll~~l~~e~vl~I~rV~K~tkgGr~~~F~alVvVGn~~G~ 84 (212)
T TIGR01020 5 LEEWVPRTKLGRLVKEGKIKSIDEIFLRNLPIKEPEIVDYLLPDLNEEEVLDVSLVQRMTDSGRRTRFRAFVVVGNRDGY 84 (212)
T ss_pred ccCeeecchhhhhhhcCCcccHHHHHHcCCCccchhhHHHHhhhcCcceEEEEEeeEEEecCCcEEEEEEEEEEeCCCCe
Confidence 456999999999999999999998 9999 99999999876 4699999999999999999999999999999999
Q ss_pred eeecccchhhHHHHHHHHHHHHHhcceEecc---------cCCcccceeeeeeeceEEEEEeecCCCCceeechHHHHHH
Q 021869 185 VGVGVAKAKEVIAAVQKSAVDARRNIVTVPM---------TKYLTFPHRSDGDFGAAKVMLRPASPGTGVIAGGAVRIVL 255 (306)
Q Consensus 185 vG~GvGKakev~~AIrKA~~~Ak~nLi~V~~---------~~~hTIphdv~gk~gstkV~L~PAP~GtGLva~~vik~Il 255 (306)
||||+|||+|+.+||+||+.+|++||++|+| +++|||||+++||||+++|+|+|||+|+||+|++++++||
T Consensus 85 vG~G~GKa~ev~~AI~kA~~~Ak~n~i~V~rg~g~w~~~~~~~hTIp~~v~Gk~gs~~V~L~PAP~GtGliag~~~r~il 164 (212)
T TIGR01020 85 VGLGIGKAKEVAPAIRKAIINAKLNIIPVRRGCGSWECGCGRPHSVPFKVTGKCGSVRVRLIPAPRGLGLVAGDVAKKVL 164 (212)
T ss_pred EeeceeecchHHHHHHHHHHHHHhCEEEEecccccccccCCCCCcEeEEEEEEEccEEEEEEeCCCCCceecCcHHHHHH
Confidence 9999999999999999999999999999999 4799999999999999999999999999999999999999
Q ss_pred HHhCccceeeeeccCC-chhhHHHHHHHHHHccC
Q 021869 256 EMAGVENALGKQLGSN-NALNNARATVVAVQKMK 288 (306)
Q Consensus 256 elAGIkD~~aKv~GSt-n~lNvaKAtf~AL~k~~ 288 (306)
++|||+||++|++||+ |++|++||||+||.+++
T Consensus 165 elAGIkDv~tk~~Gstrn~~N~~kAtf~AL~~~~ 198 (212)
T TIGR01020 165 RLAGIDDVWTQTRGETRTTVNFAKATFDALKKTY 198 (212)
T ss_pred HHcCccceeeeccCCCCChhHHHHHHHHHHHhcc
Confidence 9999999999999997 89999999999999998
No 3
>PRK04044 rps5p 30S ribosomal protein S5P; Reviewed
Probab=100.00 E-value=1.6e-57 Score=412.67 Aligned_cols=187 Identities=29% Similarity=0.480 Sum_probs=176.8
Q ss_pred CCCcccccCCCCcccccchhhhhh-ccCC-CCccccccCCc----ceeEEEEeeeeeeecCCeeEEEEEEEEecCCCCce
Q 021869 112 GPAYAGVSVLGNDVYVMDSKAKKT-SAFG-KTKKEKVKDGF----EERVVQVRRVTKVVKGGKQLKFRAIVVVGDKKGQV 185 (306)
Q Consensus 112 ~rgwsg~t~lG~~V~~~~~k~~~~-~~fs-~~ke~~i~d~f----~~~VL~i~rV~K~TkgGR~~rf~AlVvVGNgnG~v 185 (306)
.++|.|.|+|||+|++.++++.++ +.++ |++|.+|.|.| +++||+|+||||||++||++||+|||||||+||++
T Consensus 6 ~~~w~p~t~lg~lv~~~~i~s~e~i~~~~~~i~e~eivd~ll~~l~e~vv~i~rV~kvtkgGr~~sf~alVvVGn~~G~v 85 (211)
T PRK04044 6 IEEWEPKTRLGRLVKEGKITSIDEIFDSGLPIKEPEIVDVLLPDLEDEVLDINMVQRMTDSGRRVRFRVVVVVGNRDGYV 85 (211)
T ss_pred ccCccccchhhhhhhcCCcccHHHHHhcCCCcccchhhhhhhccceeEEEEEEeEEeeecCCcEEEEEEEEEEeCCCCeE
Confidence 456999999999999999999998 8899 99998888754 79999999999999999999999999999999999
Q ss_pred eecccchhhHHHHHHHHHHHHHhcceEeccc---------CCcccceeeeeeeceEEEEEeecCCCCceeechHHHHHHH
Q 021869 186 GVGVAKAKEVIAAVQKSAVDARRNIVTVPMT---------KYLTFPHRSDGDFGAAKVMLRPASPGTGVIAGGAVRIVLE 256 (306)
Q Consensus 186 G~GvGKakev~~AIrKA~~~Ak~nLi~V~~~---------~~hTIphdv~gk~gstkV~L~PAP~GtGLva~~vik~Ile 256 (306)
|+|+|||+|+.+||+||+.+|++||++|+++ ++|||||++.||||+++|+|+|||+|+||+|++.+++||+
T Consensus 86 G~G~GKa~ev~~Ai~kA~~~Akknli~V~r~~g~We~~~~~~~TI~h~v~gk~gs~~V~l~Pap~GtGiiag~~vr~vle 165 (211)
T PRK04044 86 GVGQGKAKQVGPAIRKAIRNAKLNIIKVRRGCGSWECGCGEPHSVPFKVTGKAGSVEVTLKPAPRGLGLVAGDVAKKVLE 165 (211)
T ss_pred eeeeeeccchHHHHHHHHHHHHhCeEEEEcccccccccCCCCCcCCeEEEEEEccEEEEEEECCCCCeEEECcHHHHHHH
Confidence 9999999999999999999999999999996 7899999999999999999999999999999999999999
Q ss_pred HhCccceeeeeccCC-chhhHHHHHHHHHHccC---CHHHHHHHhC
Q 021869 257 MAGVENALGKQLGSN-NALNNARATVVAVQKMK---QWREVSRERG 298 (306)
Q Consensus 257 lAGIkD~~aKv~GSt-n~lNvaKAtf~AL~k~~---S~~eiA~~rG 298 (306)
+|||+||++|++||+ |++|++||||+||.+++ ++++.++.+|
T Consensus 166 laGIkDv~aK~~Gstrn~~N~vkAt~~AL~~~~~~~~p~~~~~~~~ 211 (211)
T PRK04044 166 LAGIKDVWTRTFGETRTTVNFAKATFNALKNTYKVRTPPDWAEKRG 211 (211)
T ss_pred HcCcceEEEEccCCCCChhHHHHHHHHHHHHHHcccCHHHHHhhcC
Confidence 999999999999986 99999999999999654 5788877764
No 4
>COG0098 RpsE Ribosomal protein S5 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.7e-57 Score=399.54 Aligned_cols=160 Identities=49% Similarity=0.792 Sum_probs=158.0
Q ss_pred ccCCcceeEEEEeeeeeeecCCeeEEEEEEEEecCCCCceeecccchhhHHHHHHHHHHHHHhcceEecccCCcccceee
Q 021869 146 VKDGFEERVVQVRRVTKVVKGGKQLKFRAIVVVGDKKGQVGVGVAKAKEVIAAVQKSAVDARRNIVTVPMTKYLTFPHRS 225 (306)
Q Consensus 146 i~d~f~~~VL~i~rV~K~TkgGR~~rf~AlVvVGNgnG~vG~GvGKakev~~AIrKA~~~Ak~nLi~V~~~~~hTIphdv 225 (306)
..+.|.++||+|+||||||++||++||+|||||||+||+||||.|||+||+.||+||+..|++||++|+++++|||||++
T Consensus 20 ~~~~l~e~vv~inrV~K~~kgGRr~~F~alvVVGd~~G~VG~G~GKA~EV~~AIrKAi~~Ak~nii~V~~~~~~Tiph~v 99 (181)
T COG0098 20 EVDELLEKVVDINRVSKVVKGGRRFRFSALVVVGDRNGRVGFGIGKAKEVPEAIRKAIEDAKKNIIEVPRGNGHTIPHEV 99 (181)
T ss_pred hhhhcceeeeEEEEEEEeecCceEEEEEEEEEEeCCCCeEeeeecchhhhHHHHHHHHHHHHhCeEEEecCCCceeeeEE
Confidence 38899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeceEEEEEeecCCCCceeechHHHHHHHHhCccceeeeeccCCchhhHHHHHHHHHHccCCHHHHHHHhCCCccccc
Q 021869 226 DGDFGAAKVMLRPASPGTGVIAGGAVRIVLEMAGVENALGKQLGSNNALNNARATVVAVQKMKQWREVSRERGIPMEELW 305 (306)
Q Consensus 226 ~gk~gstkV~L~PAP~GtGLva~~vik~IlelAGIkD~~aKv~GStn~lNvaKAtf~AL~k~~S~~eiA~~rG~~vvE~~ 305 (306)
.|+||+++|.|+|||+|+||+|++++|+|||+|||+|+|+|++||+|++|++||||+||.++++++++|++||+.+.+++
T Consensus 100 ~Gk~g~~~V~L~PA~~GtGiiAGg~~r~vlelAGi~Dv~tks~GS~n~~N~vrAt~~aL~~~~~p~~ia~~Rg~~~~~~~ 179 (181)
T COG0098 100 IGKHGAVKVLLKPAPEGTGIIAGGAVRAVLELAGIKDVLAKSLGSRNPINVVRATFDALKKLRTPEDVAAKRGKKVEDIL 179 (181)
T ss_pred EEEECcEEEEEEECCCCceEEeCcHHHHHHHHcCchhhhhhccCCCChhHHHHHHHHHHHHccCHHHHHHHcCCcchhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999986
No 5
>PRK00550 rpsE 30S ribosomal protein S5; Validated
Probab=100.00 E-value=2.3e-56 Score=393.45 Aligned_cols=158 Identities=54% Similarity=0.832 Sum_probs=155.9
Q ss_pred cCCcceeEEEEeeeeeeecCCeeEEEEEEEEecCCCCceeecccchhhHHHHHHHHHHHHHhcceEecccCCcccceeee
Q 021869 147 KDGFEERVVQVRRVTKVVKGGKQLKFRAIVVVGDKKGQVGVGVAKAKEVIAAVQKSAVDARRNIVTVPMTKYLTFPHRSD 226 (306)
Q Consensus 147 ~d~f~~~VL~i~rV~K~TkgGR~~rf~AlVvVGNgnG~vG~GvGKakev~~AIrKA~~~Ak~nLi~V~~~~~hTIphdv~ 226 (306)
.++|+++||+|+||||||++||+++|+|+|+|||+||++|||+||++|+.+||+||+++|++||++|+++ +|||||++.
T Consensus 10 ~~~l~~~vl~v~rv~k~tk~Gr~~~f~alvvvGn~~G~vG~G~gKa~ev~~Ai~kA~~~A~~nl~~V~~~-~~Ti~~~v~ 88 (168)
T PRK00550 10 KLELEEKVVAINRVTKVVKGGRRFSFSALVVVGDGKGRVGFGYGKAREVPEAIRKAVEDAKKNMIKVPLV-GGTIPHEVI 88 (168)
T ss_pred cCCceEEEEEEeeeEEEecCCcEEEEEEEEEEECCCCeEeeeeeecchHHHHHHHHHHHHHhCEEEEecC-CCccceeEE
Confidence 3589999999999999999999999999999999999999999999999999999999999999999999 999999999
Q ss_pred eeeceEEEEEeecCCCCceeechHHHHHHHHhCccceeeeeccCCchhhHHHHHHHHHHccCCHHHHHHHhCCCccccc
Q 021869 227 GDFGAAKVMLRPASPGTGVIAGGAVRIVLEMAGVENALGKQLGSNNALNNARATVVAVQKMKQWREVSRERGIPMEELW 305 (306)
Q Consensus 227 gk~gstkV~L~PAP~GtGLva~~vik~IlelAGIkD~~aKv~GStn~lNvaKAtf~AL~k~~S~~eiA~~rG~~vvE~~ 305 (306)
||||+++|+|+|||+|+||+|++.++.||++|||+||++|++||+|++|++||||+||.+++|++|+|++||++++|++
T Consensus 89 gk~gs~kV~l~Pap~G~Gl~a~~~i~~il~laGI~dv~~k~~Gs~n~~n~vkA~~~aL~~~~s~~~ia~~rG~~~~~~~ 167 (168)
T PRK00550 89 GKFGAAKVLLKPASEGTGVIAGGAVRAVLELAGVKDVLAKSLGSNNPINVVRATFDALKQLRSPEEVAAKRGKSVEEIL 167 (168)
T ss_pred EEEceEEEEEEeCCCCCceEeChHHHHHHHHcCccceeeeccCCCChHHHHHHHHHHHHhCCCHHHHHHHcCCCHHHhc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999987
No 6
>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=6.5e-56 Score=385.80 Aligned_cols=154 Identities=56% Similarity=0.847 Sum_probs=151.6
Q ss_pred CcceeEEEEeeeeeeecCCeeEEEEEEEEecCCCCceeecccchhhHHHHHHHHHHHHHhcceEecccCCcccceeeeee
Q 021869 149 GFEERVVQVRRVTKVVKGGKQLKFRAIVVVGDKKGQVGVGVAKAKEVIAAVQKSAVDARRNIVTVPMTKYLTFPHRSDGD 228 (306)
Q Consensus 149 ~f~~~VL~i~rV~K~TkgGR~~rf~AlVvVGNgnG~vG~GvGKakev~~AIrKA~~~Ak~nLi~V~~~~~hTIphdv~gk 228 (306)
+|+++||+|+||||||++||+++|+|+|+|||+||++|+|+||++|+.+||+||+++|++||++|+++++ ||||+++||
T Consensus 1 ~l~e~vl~i~rv~k~tkgGr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~kA~~~Ak~nl~~V~~~~~-Ti~~~v~gk 79 (154)
T TIGR01021 1 ELEERLIAVNRVSKVVKGGRRFSFSALVVVGDGKGRVGFGFGKAKEVPDAIKKAVEKARKNLINVPLTKG-TIPHEVIGV 79 (154)
T ss_pred CceeEEEEEeeeeEEecCCcEEEEEEEEEEECCCCeEeeeeeecchHHHHHHHHHHHHHhCeEEEecCCC-ccceEEEEE
Confidence 4899999999999999999999999999999999999999999999999999999999999999999998 999999999
Q ss_pred eceEEEEEeecCCCCceeechHHHHHHHHhCccceeeeeccCCchhhHHHHHHHHHHccCCHHHHHHHhCCCccc
Q 021869 229 FGAAKVMLRPASPGTGVIAGGAVRIVLEMAGVENALGKQLGSNNALNNARATVVAVQKMKQWREVSRERGIPMEE 303 (306)
Q Consensus 229 ~gstkV~L~PAP~GtGLva~~vik~IlelAGIkD~~aKv~GStn~lNvaKAtf~AL~k~~S~~eiA~~rG~~vvE 303 (306)
||+++|+|+|||+|+||+|++.++.||++|||+||++|++||+|++|++||||+||.+++|++|+|++||+++.|
T Consensus 80 ~gs~~V~l~Pap~G~Gi~a~~~~~~il~laGI~Dv~~k~~Gs~n~~n~vkAt~~aL~~~~s~~~ia~~rG~~~~~ 154 (154)
T TIGR01021 80 SGAAKVLLKPASPGTGVIAGGAVRAILELAGVKDILAKSLGSNNPINVVRATFDALLKLKSPEDVAELRGKSVEE 154 (154)
T ss_pred ECcEEEEEEECCCCCceEeCcHHHHHHHHcCcceEEEEccCCCChHHHHHHHHHHHHcCCCHHHHHHHcCCCccC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999864
No 7
>KOG0877 consensus 40S ribosomal protein S2/30S ribosomal protein S5 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.9e-49 Score=352.12 Aligned_cols=190 Identities=30% Similarity=0.427 Sum_probs=177.7
Q ss_pred CCCcccccCCCCcccccchhhhhh-ccCC-CCccccccCCcc-----eeEEEEeeeeeeecCCeeEEEEEEEEecCCCCc
Q 021869 112 GPAYAGVSVLGNDVYVMDSKAKKT-SAFG-KTKKEKVKDGFE-----ERVVQVRRVTKVVKGGKQLKFRAIVVVGDKKGQ 184 (306)
Q Consensus 112 ~rgwsg~t~lG~~V~~~~~k~~~~-~~fs-~~ke~~i~d~f~-----~~VL~i~rV~K~TkgGR~~rf~AlVvVGNgnG~ 184 (306)
|..|.+.+.+|++++.|++++.|+ |+|| |++|.+++|.|. ++||+||+|||||++||++||+|+|+|||+||+
T Consensus 6 ~~~~~p~t~lG~lv~~~ki~sleeiyl~slpike~eiid~~lg~slkdeVLkImpVqKqtrAGQrtRfKAfVaigD~~gh 85 (213)
T KOG0877|consen 6 EKEWMPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGH 85 (213)
T ss_pred cCcCCCcccccccchhchhhhhhhhhccCccccchhhhhhhhccchHhhhheeeecccccccccccceEEEEEEeecCCc
Confidence 678999999999999999999987 9999 999999999874 799999999999999999999999999999999
Q ss_pred eeecccchhhHHHHHHHHHHHHHhcceEeccc-------CCcccceeeeeeeceEEEEEeecCCCCceeechHHHHHHHH
Q 021869 185 VGVGVAKAKEVIAAVQKSAVDARRNIVTVPMT-------KYLTFPHRSDGDFGAAKVMLRPASPGTGVIAGGAVRIVLEM 257 (306)
Q Consensus 185 vG~GvGKakev~~AIrKA~~~Ak~nLi~V~~~-------~~hTIphdv~gk~gstkV~L~PAP~GtGLva~~vik~Ilel 257 (306)
||+|+.|++|+++|||+|+++|++++++|+|+ ++||+||+++|+|+++.|.++|+|||+||++.++.+++|+|
T Consensus 86 VGlgvk~sKeva~airgaiilaklsivpvrrgyw~~~~g~pHt~~~kvtg~~~svlv~l~papRgtGivs~p~~kkll~m 165 (213)
T KOG0877|consen 86 VGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGDCGSVLVRLIPAPRGTGIVSAPVPKKLLMM 165 (213)
T ss_pred eeeeeeehHHHHHHHhHHHhhhheeeeeeeccccccccCCCccccCcccccCCcceEEEeecCCCCceeeccccHHHHHh
Confidence 99999999999999999999999999999765 69999999999999999999999999999999999999999
Q ss_pred hCccceeeeeccCCchh-hHHHHHHHHHHccCCHHHHHHHhCCCccc
Q 021869 258 AGVENALGKQLGSNNAL-NNARATVVAVQKMKQWREVSRERGIPMEE 303 (306)
Q Consensus 258 AGIkD~~aKv~GStn~l-NvaKAtf~AL~k~~S~~eiA~~rG~~vvE 303 (306)
|||+|||++++||++++ |++||+|+|++++|++ ++-.+.+..++
T Consensus 166 AGi~d~~t~~~G~t~tl~n~~ka~~~a~~~ty~~--ltp~~w~e~~~ 210 (213)
T KOG0877|consen 166 AGIDDCYTSARGCTATLGNFAKATFDAISKTYSY--LTPDLWKETVF 210 (213)
T ss_pred ccccccchhhcccchhhccHHHHHHHHHHhhhhh--hChhhcccccc
Confidence 99999999999999998 8899999999988775 55555554443
No 8
>CHL00138 rps5 ribosomal protein S5; Validated
Probab=100.00 E-value=1.2e-44 Score=311.90 Aligned_cols=122 Identities=61% Similarity=1.028 Sum_probs=120.7
Q ss_pred CCcceeEEEEeeeeeeecCCeeEEEEEEEEecCCCCceeecccchhhHHHHHHHHHHHHHhcceEecccCCcccceeeee
Q 021869 148 DGFEERVVQVRRVTKVVKGGKQLKFRAIVVVGDKKGQVGVGVAKAKEVIAAVQKSAVDARRNIVTVPMTKYLTFPHRSDG 227 (306)
Q Consensus 148 d~f~~~VL~i~rV~K~TkgGR~~rf~AlVvVGNgnG~vG~GvGKakev~~AIrKA~~~Ak~nLi~V~~~~~hTIphdv~g 227 (306)
++|+++||+|+||||||++||+++|+|||+|||+||++|+|+||+.|+.+|++||+.+|++||++|+++++|||||+++|
T Consensus 22 ~~l~ekvl~i~rV~k~tkgGR~~~f~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknl~~V~~~~~~TI~~~v~g 101 (143)
T CHL00138 22 NKWEERVIQIKRVSKVVKGGKKLSFRAIVVIGNENGWVGVGVGKADDVQNAVKKAVTDAKKNLITIPLTKSNSIPHNITG 101 (143)
T ss_pred CCceEEEEEEeeeeEEecCCcEEEEEEEEEEECCCCeEEEeeEecchHHHHHHHHHHHHHhCeEEEEcCCCCeEeeEEEE
Confidence 67999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeceEEEEEeecCCCCceeechHHHHHHHHhCccceeeeecc
Q 021869 228 DFGAAKVMLRPASPGTGVIAGGAVRIVLEMAGVENALGKQLG 269 (306)
Q Consensus 228 k~gstkV~L~PAP~GtGLva~~vik~IlelAGIkD~~aKv~G 269 (306)
|||+++|+|+|||+|+||+|++.+++||++|||+||++|+.|
T Consensus 102 k~gs~~V~l~Pap~G~Gi~a~~~i~~vlelaGI~Dv~aK~~G 143 (143)
T CHL00138 102 IFGAAKVILRPSAPGSGVIAGGSVRIVLELAGIKNILAKQLG 143 (143)
T ss_pred EEeeEEEEEEECCCCCcEEECcHHHHHHHHcCcceeEeeecC
Confidence 999999999999999999999999999999999999999987
No 9
>KOG2646 consensus Ribosomal protein S5 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.7e-43 Score=337.23 Aligned_cols=206 Identities=21% Similarity=0.259 Sum_probs=189.4
Q ss_pred CCCCCCCCCCHHHHHHHHHhhc-----CCCcccccCCCCcccccchhhhhhccCCCCccccccCCcceeEEEE--eeeee
Q 021869 90 PSFDELPMETEDEIAAAYEELY-----GPAYAGVSVLGNDVYVMDSKAKKTSAFGKTKKEKVKDGFEERVVQV--RRVTK 162 (306)
Q Consensus 90 ~~~~~~~~~~~~~~~~~~e~~~-----~rgwsg~t~lG~~V~~~~~k~~~~~~fs~~ke~~i~d~f~~~VL~i--~rV~K 162 (306)
+.=|.+....|-++++.+++|. ++||+|..|.|.+.+.++. .-....+.+|+.+.+++ ++|.+
T Consensus 127 ers~~~ke~~~~dld~~r~~~D~~~k~~~G~~~~k~~~~k~g~~~e----------~~~~~n~~Dfe~r~l~lvrr~~~~ 196 (396)
T KOG2646|consen 127 ERSDSGKENDEIDLDEERKKEDIFSKKERGHSGLKWTDTKLGLPDE----------AFRGMNYLDFELRHLELVRRRVEN 196 (396)
T ss_pred cccCcccccccchhhhhhhhhhccCchhcCCCcccccccccCCCCc----------cccCCCchhhhHHHHHHHHhhhhc
Confidence 3445555666778899999995 9999999999999999883 23345667888888887 55677
Q ss_pred eecCCeeEEEEEEEEecCCCCceeecccchh-hHHHHHHHHHHHHHhcceEecccCCcccceeeeeeeceEEEEEeecCC
Q 021869 163 VVKGGKQLKFRAIVVVGDKKGQVGVGVAKAK-EVIAAVQKSAVDARRNIVTVPMTKYLTFPHRSDGDFGAAKVMLRPASP 241 (306)
Q Consensus 163 ~TkgGR~~rf~AlVvVGNgnG~vG~GvGKak-ev~~AIrKA~~~Ak~nLi~V~~~~~hTIphdv~gk~gstkV~L~PAP~ 241 (306)
|++.|++-+++|||||||+||.+|||+||+. +...|+.+|+.+|.+||.+|+||+.|||+||+.-+|..+++.|+.+|+
T Consensus 197 ~~r~Gki~s~~~LVvvGn~nGaaG~~eGKa~~~~s~A~~ka~~rAv~~l~~ieRyE~rTiygDi~~r~~~~~l~mk~rp~ 276 (396)
T KOG2646|consen 197 QNRKGKIASMYALVVVGNGNGAAGLGEGKAADPNSPAIYKAIGRAVRNLGYIERYERRTIYGDIDDRFHEVRLDMKSRPD 276 (396)
T ss_pred cccccceeeEEEEEEEecCCcceeeccccCcCccCHHHHHHHHHHHhhcCccccccCccccccchhhhhhhhhhhhhCCC
Confidence 8899999999999999999999999999999 789999999999999999999999999999999999999999999999
Q ss_pred CCceeechHHHHHHHHhCccceeeeeccCCchhhHHHHHHHHHHccCCHHHHHHHhCCCccccc
Q 021869 242 GTGVIAGGAVRIVLEMAGVENALGKQLGSNNALNNARATVVAVQKMKQWREVSRERGIPMEELW 305 (306)
Q Consensus 242 GtGLva~~vik~IlelAGIkD~~aKv~GStn~lNvaKAtf~AL~k~~S~~eiA~~rG~~vvE~~ 305 (306)
|+||+||+++++||++|||+|+++|+.||+|-+|+++|+|+||..|++++|+|.+||+||||++
T Consensus 277 GfGLrcn~il~kIC~~~GIKDis~kv~GsrN~m~i~k~~~e~l~~qet~qqlA~rkG~hvVdVr 340 (396)
T KOG2646|consen 277 GFGLRCNPILIKICECAGIKDISGKVKGSRNEMNITKAAFEALALQETHQQLAYRKGLHVVDVR 340 (396)
T ss_pred cccccccHHHHHHHHHhccccccceeeccchHHHHHHHHHHHHhhhhhhHHHHHhcCCeEEEec
Confidence 9999999999999999999999999999999999999999999999999999999999999985
No 10
>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=99.95 E-value=6.9e-28 Score=187.03 Aligned_cols=74 Identities=45% Similarity=0.809 Sum_probs=73.0
Q ss_pred eeeeeceEEEEEeecCCCCceeechHHHHHHHHhCccceeeeeccCCchhhHHHHHHHHHHccCCHHHHHHHhC
Q 021869 225 SDGDFGAAKVMLRPASPGTGVIAGGAVRIVLEMAGVENALGKQLGSNNALNNARATVVAVQKMKQWREVSRERG 298 (306)
Q Consensus 225 v~gk~gstkV~L~PAP~GtGLva~~vik~IlelAGIkD~~aKv~GStn~lNvaKAtf~AL~k~~S~~eiA~~rG 298 (306)
|.||||+++|+|+|+|+|+||+||+.++.||++|||+||++|++||+|++|++||||+||.+++|++|+|++||
T Consensus 1 V~gk~g~~~V~l~Pap~G~Gl~a~~~vr~il~laGI~Dv~~K~~Gs~n~~n~v~A~~~aL~~~~s~~~ia~~rG 74 (74)
T PF03719_consen 1 VTGKFGATKVFLKPAPPGTGLVAGGAVRAILELAGIKDVYAKSRGSRNPINVVKATFKALKNQRSPEDIAEKRG 74 (74)
T ss_dssp EEEEETTEEEEEEESCTTSCEESSHHHHHHHHHTTESSEEEEEESBSSHHHHHHHHHHHHHTSCSHHHHHHHTT
T ss_pred CEEEEeeEEEEEEeCCCCcceeechhHHHHHHhcccccEEeeccCCCChhhHHHHHHHHHHhcCCHHHHHHhcC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999998
No 11
>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=99.90 E-value=3.6e-24 Score=163.65 Aligned_cols=67 Identities=49% Similarity=0.831 Sum_probs=64.6
Q ss_pred CcceeEEEEeeeeeeecCCeeEEEEEEEEecCCCCceeecccchhhHHHHHHHHHHHHHhcceEecc
Q 021869 149 GFEERVVQVRRVTKVVKGGKQLKFRAIVVVGDKKGQVGVGVAKAKEVIAAVQKSAVDARRNIVTVPM 215 (306)
Q Consensus 149 ~f~~~VL~i~rV~K~TkgGR~~rf~AlVvVGNgnG~vG~GvGKakev~~AIrKA~~~Ak~nLi~V~~ 215 (306)
+|+++||+++||++||++||+++|+|||+|||+||++|||+||+.|+..|++||.++|++||++|+|
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 5899999999999999999999999999999999999999999999999999999999999999986
No 12
>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=54.75 E-value=48 Score=23.12 Aligned_cols=39 Identities=28% Similarity=0.285 Sum_probs=26.2
Q ss_pred CeeEEEEEEEEecCCCCceeecccchhhHHHHHHHHHHHHHhc
Q 021869 167 GKQLKFRAIVVVGDKKGQVGVGVAKAKEVIAAVQKSAVDARRN 209 (306)
Q Consensus 167 GR~~rf~AlVvVGNgnG~vG~GvGKakev~~AIrKA~~~Ak~n 209 (306)
+....|.+-|.+++ -..+.|.|+ .-.+|-+.|-..|.+.
T Consensus 29 ~~~~~f~~~v~i~~--~~~~~g~g~--sKk~Ak~~AA~~al~~ 67 (68)
T cd00048 29 DHAPRFTVEVTVGG--KITGEGEGS--SKKEAKQNAAEAALRK 67 (68)
T ss_pred CCCCeEEEEEEECC--EEEEEeecC--CHHHHHHHHHHHHHHh
Confidence 33568888888876 356666665 4456777777776654
No 13
>smart00358 DSRM Double-stranded RNA binding motif.
Probab=45.89 E-value=61 Score=22.71 Aligned_cols=40 Identities=28% Similarity=0.350 Sum_probs=26.3
Q ss_pred CeeEEEEEEEEecCCCCceeecccchhhHHHHHHHHHHHHHhcc
Q 021869 167 GKQLKFRAIVVVGDKKGQVGVGVAKAKEVIAAVQKSAVDARRNI 210 (306)
Q Consensus 167 GR~~rf~AlVvVGNgnG~vG~GvGKakev~~AIrKA~~~Ak~nL 210 (306)
+....|.+-|.+++. .+|-|.|++ -.+|-+.|...|.+.|
T Consensus 27 ~~~~~f~~~v~i~~~--~~~~g~g~s--Kk~Ak~~AA~~al~~L 66 (67)
T smart00358 27 DHAPRFTVTVKVGGE--YTGEGEGSS--KKEAKQRAAEAALRSL 66 (67)
T ss_pred CCCCcEEEEEEECCE--EEEEeccCC--HHHHHHHHHHHHHHhc
Confidence 334578888888653 555555554 4567788887777655
No 14
>PF14493 HTH_40: Helix-turn-helix domain
Probab=44.27 E-value=28 Score=27.40 Aligned_cols=27 Identities=26% Similarity=0.256 Sum_probs=23.2
Q ss_pred HHHHHHHHHHccCCHHHHHHHhCCCcc
Q 021869 276 NARATVVAVQKMKQWREVSRERGIPME 302 (306)
Q Consensus 276 vaKAtf~AL~k~~S~~eiA~~rG~~vv 302 (306)
...-|++-+.+..|.++||+.||++..
T Consensus 2 t~~~T~~l~~~G~si~eIA~~R~L~~s 28 (91)
T PF14493_consen 2 TAQITYELFQKGLSIEEIAKIRGLKES 28 (91)
T ss_pred HHHHHHHHHHcCCCHHHHHHHcCCCHH
Confidence 356788899999999999999999764
No 15
>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=43.99 E-value=20 Score=33.68 Aligned_cols=132 Identities=13% Similarity=0.036 Sum_probs=70.3
Q ss_pred ccCCCCCCCCCCCCCCCCCC--CCCCHHHHHHHHHhhcCCCcccccCCCCcccccchhhhhhccCCCCccccccCCcce-
Q 021869 76 VFDPPTPPEDYTPPPSFDEL--PMETEDEIAAAYEELYGPAYAGVSVLGNDVYVMDSKAKKTSAFGKTKKEKVKDGFEE- 152 (306)
Q Consensus 76 ~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~e~~~~rgwsg~t~lG~~V~~~~~k~~~~~~fs~~ke~~i~d~f~~- 152 (306)
++.+..++++++..+.-.-. -.--||-+..+.-|+.||--....|.++. ..+.+. . ..+.....+.+.+..
T Consensus 95 ~~~~~~~~~~~~~~~~S~G~A~g~s~~eA~~~al~E~iERda~~~~w~~~~-~~~~i~--~---~~~~~~~~~~~~~~~~ 168 (332)
T PF02624_consen 95 VFYPYRDGEPLFFYSTSNGLAAGNSLEEAILHALLEVIERDAFSLWWYNRL-PPPRID--D---VLDPTLPELLERLERL 168 (332)
T ss_pred hcCCCCCcccccccCCCCEEcCCCCHHHHHHHHHHHHHHHHHHHHHHHhcC-CCCeEe--c---ccCcCCHHHHHHHHHh
Confidence 34444445555554443321 12346678888888988877777776662 222210 0 000111122222211
Q ss_pred --eEEEEeeeeeeecCCeeEEEEEEE-EecCCCCceeecccchhhHHHHHHHHHHHHHhcceEec
Q 021869 153 --RVVQVRRVTKVVKGGKQLKFRAIV-VVGDKKGQVGVGVAKAKEVIAAVQKSAVDARRNIVTVP 214 (306)
Q Consensus 153 --~VL~i~rV~K~TkgGR~~rf~AlV-vVGNgnG~vG~GvGKakev~~AIrKA~~~Ak~nLi~V~ 214 (306)
.-+++.-. ..|......-+-|++ ...+..+..-+|.|++.+...|+.||+..|.+......
T Consensus 169 ~~~~~~v~l~-dit~~~~vpv~~a~~~~~~~~~~~~~~G~ga~~~~~~Al~rAl~E~~q~~~~~~ 232 (332)
T PF02624_consen 169 REAGLEVRLF-DITNDFGVPVVAAVLRNEDKDRPYYAVGAGAHLDPEEALERALTEAAQSRLLFI 232 (332)
T ss_pred hcCceEEEEE-ECCCCCCceEEEEEEEecCCCCcceEEEeccCCCHHHHHHHHHHHHHHHHHHHH
Confidence 22222222 223333444333333 12356777899999999999999999999988766554
No 16
>PF00035 dsrm: Double-stranded RNA binding motif; InterPro: IPR001159 The DsRBD domain is found in a variety of RNA-binding proteins with different structures and exhibiting a diversity of functions []. It is involved in localisation of at least five different mRNAs in the early Drosophila embryo and by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.; GO: 0003725 double-stranded RNA binding, 0005622 intracellular; PDB: 1EKZ_A 1STU_A 1QU6_A 2L2M_A 3ADJ_A 1WHN_A 3LLH_B 2B7V_A 2L3J_A 1UHZ_A ....
Probab=43.16 E-value=1e+02 Score=21.78 Aligned_cols=43 Identities=19% Similarity=0.211 Sum_probs=27.8
Q ss_pred ecCCeeEEEEEEEEecCCCCceeecccchhhHHHHHHHHHHHHHhcc
Q 021869 164 VKGGKQLKFRAIVVVGDKKGQVGVGVAKAKEVIAAVQKSAVDARRNI 210 (306)
Q Consensus 164 TkgGR~~rf~AlVvVGNgnG~vG~GvGKakev~~AIrKA~~~Ak~nL 210 (306)
+..+...+|.+-|.+++ =.+|.|.|++ -..|-+.|-..|.+.|
T Consensus 25 ~~~~~~~~f~~~~~i~~--~~~~~g~g~s--Kk~Ak~~AA~~al~~L 67 (67)
T PF00035_consen 25 GPSHHRPRFICTVYIDG--KEYGEGEGSS--KKEAKQQAAKKALQKL 67 (67)
T ss_dssp SSSSSSEEEEEEEEETT--EEEEEEEESS--HHHHHHHHHHHHHHHH
T ss_pred CCCCCCceEEEEEEECC--EEEeEeccCC--HHHHHHHHHHHHHHhC
Confidence 34455458888888854 3456566654 4678788877776543
No 17
>cd01684 Tet_like_IV EF-G_domain IV_RPP domain is a part of bacterial ribosomal protected proteins (RPP) family. RPPs such as tetracycline resistance proteins Tet(M) and Tet(O) mediate tetracycline resistance in both gram-positive and -negative species. Tetracyclines inhibit the accommodation of aminoacyl-tRNA into ribosomal A site and therefore prevent the addition of new amino acids to the growing polypeptide. RPPs Tet(M) confer tetracycline resistance by releasing tetracycline from the ribosome and thereby freeing the ribosome from inhibitory effects of the drug, such that aa-tRNA can bind to the A site and protein synthesis can continue.
Probab=40.00 E-value=90 Score=25.59 Aligned_cols=18 Identities=17% Similarity=0.492 Sum_probs=15.6
Q ss_pred eceEEEEEeecCCCCcee
Q 021869 229 FGAAKVMLRPASPGTGVI 246 (306)
Q Consensus 229 ~gstkV~L~PAP~GtGLv 246 (306)
|+.+.+.|.|.++|.|+.
T Consensus 25 ~a~v~l~veP~~~g~g~~ 42 (115)
T cd01684 25 WATVGLRVEPLPRGSGLQ 42 (115)
T ss_pred EEEEEEEEEECCCCCCcE
Confidence 999999999999986553
No 18
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=39.25 E-value=47 Score=28.99 Aligned_cols=55 Identities=24% Similarity=0.305 Sum_probs=38.8
Q ss_pred hHHHHHHHHhCccceeeeeccCCchh----hHHHHHHHHHHccCCHHHHHHHhCCCcccc
Q 021869 249 GAVRIVLEMAGVENALGKQLGSNNAL----NNARATVVAVQKMKQWREVSRERGIPMEEL 304 (306)
Q Consensus 249 ~vik~IlelAGIkD~~aKv~GStn~l----NvaKAtf~AL~k~~S~~eiA~~rG~~vvE~ 304 (306)
.+++ -++-+||+.+-.|..|.-.+- |..--.-+.|.+..++++|++-.|+.+--+
T Consensus 68 kvlk-aleq~gI~vIPvk~KgrGrprkyd~~t~~~i~emlr~gk~preIsk~lGIpirTv 126 (139)
T COG1710 68 KVLK-ALEQMGIKVIPVKLKGRGRPRKYDRNTLLRIREMLRNGKTPREISKDLGIPIRTV 126 (139)
T ss_pred HHHH-HHHhCCceEeeeeecCCCCCcccchhHHHHHHHHHHcCCCHHHHHHhhCCchhhh
Confidence 3444 455669999998877743333 333345577888999999999999987543
No 19
>PF06207 DUF1002: Protein of unknown function (DUF1002); InterPro: IPR009343 This protein family has no known function. Its members are about 300 amino acids in length. It has so far been detected in Firmicute bacteria and some archaebacteria.
Probab=34.85 E-value=64 Score=30.36 Aligned_cols=38 Identities=21% Similarity=0.179 Sum_probs=30.7
Q ss_pred EEEEeecCCCCceeech------------HHHHHHHHhCccceeeeeccC
Q 021869 233 KVMLRPASPGTGVIAGG------------AVRIVLEMAGVENALGKQLGS 270 (306)
Q Consensus 233 kV~L~PAP~GtGLva~~------------vik~IlelAGIkD~~aKv~GS 270 (306)
-+++.|..+|.||...- ..+.-|..|||+||..++-.-
T Consensus 54 Sa~V~~~~~g~Gi~V~i~tp~NIt~VT~~mY~NAl~TAGv~da~I~Vasp 103 (225)
T PF06207_consen 54 SAYVTPTDKGSGIKVEIVTPNNITWVTEEMYANALITAGVTDADIYVASP 103 (225)
T ss_pred EEEEEECCCCCCeEEEEeccCcceeecHHHHHHHHHHcCCCcceEEEecc
Confidence 45677899999987754 678889999999999988543
No 20
>CHL00130 rbcS ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit; Reviewed
Probab=28.18 E-value=48 Score=29.27 Aligned_cols=27 Identities=22% Similarity=0.214 Sum_probs=23.7
Q ss_pred CCCCCCCCHHHHHHHHHhhcCCCcccc
Q 021869 92 FDELPMETEDEIAAAYEELYGPAYAGV 118 (306)
Q Consensus 92 ~~~~~~~~~~~~~~~~e~~~~rgwsg~ 118 (306)
|.=+|+-|.|+|..|.+-++..||++.
T Consensus 8 fSyLPpLTdeqI~kQI~Y~i~~GW~p~ 34 (138)
T CHL00130 8 FSFLPDLTDQQIEKQIQYAISKGWALN 34 (138)
T ss_pred eccCCCCCHHHHHHHHHHHHhcCCeEE
Confidence 455788999999999999999999964
No 21
>PLN02289 ribulose-bisphosphate carboxylase small chain
Probab=26.79 E-value=48 Score=30.34 Aligned_cols=27 Identities=22% Similarity=0.311 Sum_probs=23.7
Q ss_pred CCCCCCCCHHHHHHHHHhhcCCCcccc
Q 021869 92 FDELPMETEDEIAAAYEELYGPAYAGV 118 (306)
Q Consensus 92 ~~~~~~~~~~~~~~~~e~~~~rgwsg~ 118 (306)
|--+|+-|+|+|+.|.|-++..||.+.
T Consensus 70 fSYLPpLtdeqI~kQVeYli~~GW~pc 96 (176)
T PLN02289 70 LSYLPDLTDEELAKEVDYLLRNKWVPC 96 (176)
T ss_pred eecCCCCCHHHHHHHHHHHHhCCCeee
Confidence 445788899999999999999999875
No 22
>PRK12371 ribonuclease III; Reviewed
Probab=25.87 E-value=1.2e+02 Score=28.33 Aligned_cols=40 Identities=20% Similarity=0.077 Sum_probs=27.2
Q ss_pred CeeEEEEEEEEecCCCCceeecccchhhHHHHHHHHHHHHHhcc
Q 021869 167 GKQLKFRAIVVVGDKKGQVGVGVAKAKEVIAAVQKSAVDARRNI 210 (306)
Q Consensus 167 GR~~rf~AlVvVGNgnG~vG~GvGKakev~~AIrKA~~~Ak~nL 210 (306)
+....|.+-|.+||.. .|.|.| ..-..|-+.|-.+|..+|
T Consensus 190 ~h~~~F~v~v~v~~~~--~~~g~G--~sKK~Ae~~AA~~al~~~ 229 (235)
T PRK12371 190 DHDPRFTVEVEVKGFA--PETGEG--RSKRAAEQVAAEKMLERE 229 (235)
T ss_pred CCCCeEEEEEEECCEE--EEEeee--CCHHHHHHHHHHHHHHHh
Confidence 4557888888887653 444444 445678888888887665
No 23
>cd03527 RuBisCO_small Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits.
Probab=25.24 E-value=61 Score=26.91 Aligned_cols=27 Identities=26% Similarity=0.407 Sum_probs=22.9
Q ss_pred CCCCCCCCHHHHHHHHHhhcCCCcccc
Q 021869 92 FDELPMETEDEIAAAYEELYGPAYAGV 118 (306)
Q Consensus 92 ~~~~~~~~~~~~~~~~e~~~~rgwsg~ 118 (306)
|.-+|+-|.|||.++-+-++..||...
T Consensus 6 ~sylp~lt~~~i~~QI~yll~qG~~~~ 32 (99)
T cd03527 6 FSYLPPLTDEQIAKQIDYIISNGWAPC 32 (99)
T ss_pred cccCCCCCHHHHHHHHHHHHhCCCEEE
Confidence 445778899999999999999999854
No 24
>cd01434 EFG_mtEFG1_IV EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provi
Probab=24.66 E-value=2.1e+02 Score=23.07 Aligned_cols=21 Identities=24% Similarity=0.596 Sum_probs=17.5
Q ss_pred eeeeceEEEEEeecCCCCcee
Q 021869 226 DGDFGAAKVMLRPASPGTGVI 246 (306)
Q Consensus 226 ~gk~gstkV~L~PAP~GtGLv 246 (306)
.++|+.+.+.+.|+++|.|+.
T Consensus 22 ~~~~a~v~l~v~P~~~g~g~~ 42 (116)
T cd01434 22 AGQYGHVVLEIEPLPRGSGFE 42 (116)
T ss_pred CCeEEEEEEEEEECCCCCCCE
Confidence 356999999999999997764
No 25
>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=23.82 E-value=1.1e+02 Score=23.46 Aligned_cols=42 Identities=21% Similarity=0.328 Sum_probs=30.1
Q ss_pred CCeeEEEEEEEEecCCCCceeecccchhhHHHHHHHHHHHHHhcc
Q 021869 166 GGKQLKFRAIVVVGDKKGQVGVGVAKAKEVIAAVQKSAVDARRNI 210 (306)
Q Consensus 166 gGR~~rf~AlVvVGNgnG~vG~GvGKakev~~AIrKA~~~Ak~nL 210 (306)
+|..++..+-+ ...|..=.+.+.+.++-.||+.|+....+.|
T Consensus 46 ~~~~~~v~i~i---~~~~~~l~a~~~~~d~~~Aid~a~dkl~rql 87 (97)
T PF02482_consen 46 EGKGYRVEITI---HVPGHVLVAEESAEDLYAAIDEAFDKLERQL 87 (97)
T ss_dssp ETTEEEEEEEE---EETTEEEEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred cCCCEEEEEEE---EeCCceEEEEEecCCHHHHHHHHHHHHHHHH
Confidence 34444444444 3356666788899999999999999888765
No 26
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=22.94 E-value=1.6e+02 Score=20.21 Aligned_cols=35 Identities=11% Similarity=0.210 Sum_probs=26.5
Q ss_pred cCCchhhHHHHHHHHHHccCCHHHHHHHhCCCccc
Q 021869 269 GSNNALNNARATVVAVQKMKQWREVSRERGIPMEE 303 (306)
Q Consensus 269 GStn~lNvaKAtf~AL~k~~S~~eiA~~rG~~vvE 303 (306)
+|+-+..+.....+.+....|..+||+..|..-.-
T Consensus 9 ~~r~T~~~~~~i~~~~~~~~s~~~vA~~~~vs~~T 43 (52)
T PF13542_consen 9 YCRITKRLEQYILKLLRESRSFKDVARELGVSWST 43 (52)
T ss_pred CCcHHHHHHHHHHHHHhhcCCHHHHHHHHCCCHHH
Confidence 45555566777778888778999999999987543
No 27
>COG3360 Uncharacterized conserved protein [Function unknown]
Probab=22.60 E-value=1.5e+02 Score=23.46 Aligned_cols=23 Identities=13% Similarity=0.124 Sum_probs=18.8
Q ss_pred hHHHHHHHHHHHHHhcceEeccc
Q 021869 194 EVIAAVQKSAVDARRNIVTVPMT 216 (306)
Q Consensus 194 ev~~AIrKA~~~Ak~nLi~V~~~ 216 (306)
.+..|++.|+.+|...+..++-.
T Consensus 18 S~d~Ai~~Ai~RA~~t~~~l~wf 40 (71)
T COG3360 18 SIDAAIANAIARAADTLDNLDWF 40 (71)
T ss_pred cHHHHHHHHHHHHHhhhhcceEE
Confidence 37889999999999888777544
No 28
>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=22.20 E-value=4.7e+02 Score=22.61 Aligned_cols=12 Identities=8% Similarity=0.648 Sum_probs=8.9
Q ss_pred CCcceeEEEEee
Q 021869 148 DGFEERVVQVRR 159 (306)
Q Consensus 148 d~f~~~VL~i~r 159 (306)
++|..+++.+..
T Consensus 49 ngWs~~i~~~~~ 60 (154)
T PF04098_consen 49 NGWSSEIISLEQ 60 (154)
T ss_dssp TTEEEEEEEEEE
T ss_pred CCCceEEEeeEe
Confidence 577778877766
No 29
>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=22.10 E-value=1.4e+02 Score=26.47 Aligned_cols=38 Identities=26% Similarity=0.246 Sum_probs=26.4
Q ss_pred eEEEEEEEEecCCCCceeecccchhhHHHHHHHHHHHHHhcc
Q 021869 169 QLKFRAIVVVGDKKGQVGVGVAKAKEVIAAVQKSAVDARRNI 210 (306)
Q Consensus 169 ~~rf~AlVvVGNgnG~vG~GvGKakev~~AIrKA~~~Ak~nL 210 (306)
...|.+-|.+++ -.+|-|.|+ ....|-+.|..+|.+.|
T Consensus 183 ~~~f~~~v~~~~--~~~~~g~g~--skk~A~~~AA~~Al~~l 220 (220)
T TIGR02191 183 DKEFTVEVSVNG--EPYGEGKGK--SKKEAEQNAAKAALEKL 220 (220)
T ss_pred CceEEEEEEECC--EEEEEeeeC--CHHHHHHHHHHHHHHhC
Confidence 357888888873 345655554 45788888888887654
No 30
>PRK13832 plasmid partitioning protein; Provisional
Probab=21.36 E-value=2.6e+02 Score=29.71 Aligned_cols=69 Identities=19% Similarity=0.104 Sum_probs=47.5
Q ss_pred EeecCCC---CceeechHHHHHHHHhCccceeeeeccCCch------h--hH----------HHHHHHHHHccCCHHHHH
Q 021869 236 LRPASPG---TGVIAGGAVRIVLEMAGVENALGKQLGSNNA------L--NN----------ARATVVAVQKMKQWREVS 294 (306)
Q Consensus 236 L~PAP~G---tGLva~~vik~IlelAGIkD~~aKv~GStn~------l--Nv----------aKAtf~AL~k~~S~~eiA 294 (306)
++|.+.| +.|++|..=..-+.++|.+.+-+.++-..+. + |+ ++|+-.-+...+|.++||
T Consensus 46 VRp~~dg~g~YeIIAGeRRlrAa~~aGl~~IPviV~d~dDd~a~~~SL~ENiQRedL~PiEea~AfkrLie~G~T~EeIA 125 (520)
T PRK13832 46 VSPEEDGGNGYIIQAGHRRVKQAIAAGLEEIEVLVTEAANDNGAMRSMVENIAREPLNPVDQWRAIERLVALGWTEEAIA 125 (520)
T ss_pred EEecCCCCccEEEccCHHHHHHHHHCCCCeeeEEEEeCCcHHHHHHHHHHHhCcCCCCHHHHHHHHHHHHhcCCCHHHHH
Confidence 3455544 6799988777778999999888887533211 1 33 345555556788999999
Q ss_pred HHhCCCcccc
Q 021869 295 RERGIPMEEL 304 (306)
Q Consensus 295 ~~rG~~vvE~ 304 (306)
...|++...+
T Consensus 126 ~~lG~S~~~V 135 (520)
T PRK13832 126 VALALPVRQI 135 (520)
T ss_pred HHHCCCHHHH
Confidence 9999886554
No 31
>cd07018 S49_SppA_67K_type Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 67K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily contain an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Unlike the eukaryotic functional homologs that are proposed to be aspartic proteases, site-directed mutagenesis and sequence analysis have shown that members in this subfamily, mostly bacterial, are serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys
Probab=21.17 E-value=4.6e+02 Score=23.75 Aligned_cols=125 Identities=18% Similarity=0.209 Sum_probs=65.8
Q ss_pred EEEEEEEEecCCCCceeecccchhhHHHHHHHHHHHHHhcce-EecccCCcccceeeeeeeceEEEEEeecCCCCcee--
Q 021869 170 LKFRAIVVVGDKKGQVGVGVAKAKEVIAAVQKSAVDARRNIV-TVPMTKYLTFPHRSDGDFGAAKVMLRPASPGTGVI-- 246 (306)
Q Consensus 170 ~rf~AlVvVGNgnG~vG~GvGKakev~~AIrKA~~~Ak~nLi-~V~~~~~hTIphdv~gk~gstkV~L~PAP~GtGLv-- 246 (306)
.+.+++|+.+|.-|- +...+.++..+++.- +.+.+.++ ++... .+--+-+- +.+-+|.+.|.- ..|++
T Consensus 45 ~~ik~vvL~~~s~gg---~~~~~~el~~~i~~~-~~~~kpVia~~~~~--~sggy~la--saad~I~a~p~~-~vg~iGv 115 (222)
T cd07018 45 DRIKGIVLDLDGLSG---GLAKLEELRQALERF-RASGKPVIAYADGY--SQGQYYLA--SAADEIYLNPSG-SVELTGL 115 (222)
T ss_pred CCeEEEEEECCCCCC---CHHHHHHHHHHHHHH-HHhCCeEEEEeCCC--Cchhhhhh--hhCCEEEECCCc-eEEeecc
Confidence 367888888876543 777788888888753 22334433 22211 00000111 123355554432 24443
Q ss_pred --echHHHHHHHHhCccceeeeeccCC----chh------hHHHHHHHHHHc-cCC--HHHHHHHhCCCcccc
Q 021869 247 --AGGAVRIVLEMAGVENALGKQLGSN----NAL------NNARATVVAVQK-MKQ--WREVSRERGIPMEEL 304 (306)
Q Consensus 247 --a~~vik~IlelAGIkD~~aKv~GSt----n~l------NvaKAtf~AL~k-~~S--~~eiA~~rG~~vvE~ 304 (306)
-+.-.+.+++..||+-=..++ |.- +++ --.|..++++.. .+. .+.+|+.||+...++
T Consensus 116 ~~~~~~~~~ll~klGv~~~~~~~-G~~K~~~~~~~~~~~s~~~r~~~~~~l~~~~~~f~~~Va~~R~~~~~~~ 187 (222)
T cd07018 116 SAETLFFKGLLDKLGVEVQVFRV-GEYKSAVEPFTRDDMSPEAREQTQALLDSLWDQYLADVAASRGLSPDAL 187 (222)
T ss_pred chhhhhHHHHHHHcCCcEEEEEE-eccccccchhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHH
Confidence 245679999999999654443 221 122 113344443332 222 577888888765543
No 32
>PRK00102 rnc ribonuclease III; Reviewed
Probab=20.79 E-value=1.9e+02 Score=25.88 Aligned_cols=38 Identities=24% Similarity=0.302 Sum_probs=26.6
Q ss_pred eEEEEEEEEecCCCCceeecccchhhHHHHHHHHHHHHHhcc
Q 021869 169 QLKFRAIVVVGDKKGQVGVGVAKAKEVIAAVQKSAVDARRNI 210 (306)
Q Consensus 169 ~~rf~AlVvVGNgnG~vG~GvGKakev~~AIrKA~~~Ak~nL 210 (306)
...|.+-|.+++ -.+|.|.|+ ....|-+.|..+|.++|
T Consensus 189 ~~~f~~~v~i~~--~~~~~g~g~--skk~Ae~~AA~~Al~~l 226 (229)
T PRK00102 189 DKEFTVEVTVNG--KELGEGTGS--SKKEAEQAAAKQALKKL 226 (229)
T ss_pred CceEEEEEEECC--EEEEEeeeC--CHHHHHHHHHHHHHHHH
Confidence 356788888874 246666555 55688888888888765
No 33
>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=20.50 E-value=75 Score=25.51 Aligned_cols=21 Identities=24% Similarity=0.409 Sum_probs=15.1
Q ss_pred ceeecccchhh-HHHHHHHHHH
Q 021869 184 QVGVGVAKAKE-VIAAVQKSAV 204 (306)
Q Consensus 184 ~vG~GvGKake-v~~AIrKA~~ 204 (306)
++|+|.+++.+ +.+|+++|+.
T Consensus 4 ~iGiG~a~G~~r~~~Av~~Al~ 25 (95)
T PF12327_consen 4 MIGIGEASGENRAEEAVEQALN 25 (95)
T ss_dssp EEEEEEEESTTHHHHHHHHHHT
T ss_pred EEEEEEECCccHHHHHHHHHHh
Confidence 57888888876 5666666654
No 34
>cd00308 enolase_like Enolase-superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. Enolase superfamily contains different enzymes, like enolases, glutarate-, fucanate- and galactonate dehydratases, o-succinylbenzoate synthase, N-acylamino acid racemase, L-alanine-DL-glutamate epimerase, mandelate racemase, muconate lactonizing enzyme and 3-methylaspartase.
Probab=20.29 E-value=1.2e+02 Score=27.36 Aligned_cols=39 Identities=23% Similarity=0.350 Sum_probs=27.9
Q ss_pred EEEEEEecCCCCceeecccchhhHHHHHHHHHHHHHhcceEecc
Q 021869 172 FRAIVVVGDKKGQVGVGVAKAKEVIAAVQKSAVDARRNIVTVPM 215 (306)
Q Consensus 172 f~AlVvVGNgnG~vG~GvGKakev~~AIrKA~~~Ak~nLi~V~~ 215 (306)
-..+|-+=..+|.+|+|.. ..||+-|..++.-...-+|+
T Consensus 25 ~~~iv~l~~~~G~~G~Ge~-----~~aid~Al~Dl~gk~~~~pl 63 (229)
T cd00308 25 DTVLVKLTTDSGVVGWGEV-----ISGIDMALWDLAAKALGVPL 63 (229)
T ss_pred eeEEEEEEECCCCcchhhH-----HHHHHHHHHHHhHhHcCCcH
Confidence 3455556567799999977 78999999877655544554
Done!