Query psy10165
Match_columns 337
No_of_seqs 164 out of 1095
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 19:31:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10165.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10165hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK04044 rps5p 30S ribosomal p 100.0 4.4E-55 9.5E-60 401.4 19.8 193 67-285 6-211 (211)
2 PTZ00070 40S ribosomal protein 100.0 6E-55 1.3E-59 408.3 17.0 187 66-277 33-228 (257)
3 TIGR01020 rpsE_arch ribosomal 100.0 1.3E-54 2.7E-59 398.2 17.4 183 67-275 5-198 (212)
4 PRK00550 rpsE 30S ribosomal pr 100.0 1.5E-53 3.2E-58 380.3 20.0 157 134-292 11-167 (168)
5 TIGR01021 rpsE_bact ribosomal 100.0 3.3E-53 7.1E-58 373.5 19.4 153 135-289 1-153 (154)
6 COG0098 RpsE Ribosomal protein 100.0 4E-53 8.7E-58 378.9 18.5 159 133-292 21-179 (181)
7 KOG2646|consensus 100.0 9.4E-54 2E-58 414.2 6.7 269 4-322 97-378 (396)
8 CHL00138 rps5 ribosomal protei 100.0 2.3E-42 5E-47 301.3 16.2 123 133-256 21-143 (143)
9 KOG0877|consensus 100.0 4.8E-41 1E-45 304.7 10.7 189 64-277 3-199 (213)
10 PF03719 Ribosomal_S5_C: Ribos 99.9 5.2E-27 1.1E-31 184.2 9.4 74 212-285 1-74 (74)
11 PF00333 Ribosomal_S5: Ribosom 99.9 6.6E-23 1.4E-27 158.4 8.4 67 135-202 1-67 (67)
12 smart00358 DSRM Double-strande 39.6 73 0.0016 22.7 4.7 39 155-197 28-66 (67)
13 PF14493 HTH_40: Helix-turn-he 38.0 39 0.00084 26.9 3.3 30 263-292 2-31 (91)
14 cd00048 DSRM Double-stranded R 37.7 1.1E+02 0.0024 21.5 5.4 39 154-196 29-67 (68)
15 PF01990 ATP-synt_F: ATP synth 34.7 33 0.00071 27.6 2.4 71 232-307 3-78 (95)
16 COG1710 Uncharacterized protei 34.2 69 0.0015 28.2 4.3 57 233-289 64-124 (139)
17 cd00674 LysRS_core_class_I cat 34.0 95 0.0021 31.4 6.0 131 168-306 29-174 (353)
18 PF00035 dsrm: Double-stranded 32.9 1.8E+02 0.004 20.7 6.0 40 153-196 27-66 (67)
19 PF06207 DUF1002: Protein of u 29.1 84 0.0018 29.9 4.4 39 219-257 53-103 (225)
20 cd01684 Tet_like_IV EF-G_domai 26.6 1.6E+02 0.0034 24.5 5.2 42 215-272 24-65 (115)
21 KOG4328|consensus 26.5 1E+02 0.0022 32.5 4.8 35 139-175 174-215 (498)
22 PRK13832 plasmid partitioning 24.6 2.7E+02 0.006 29.9 7.6 71 223-293 46-137 (520)
23 PF06754 PhnG: Phosphonate met 24.4 1.7E+02 0.0036 26.0 5.2 42 153-196 59-100 (146)
24 PF02624 YcaO: YcaO-like famil 23.0 1.1E+02 0.0023 29.3 4.0 35 167-201 198-232 (332)
25 TIGR00607 rad52 recombination 21.6 2.9E+02 0.0064 25.2 6.2 73 119-193 26-109 (161)
26 COG0350 Ada Methylated DNA-pro 20.8 1.5E+02 0.0032 26.7 4.2 69 261-329 87-166 (168)
27 cd07018 S49_SppA_67K_type Sign 20.6 5.2E+02 0.011 23.7 7.9 132 153-292 41-188 (222)
No 1
>PRK04044 rps5p 30S ribosomal protein S5P; Reviewed
Probab=100.00 E-value=4.4e-55 Score=401.41 Aligned_cols=193 Identities=23% Similarity=0.379 Sum_probs=181.9
Q ss_pred CCCCCCCCCCCccCCCCCCCCCChhhhhhhccccccccccccCCCCCCCcccccccCcccccccccCCCcceEEEEEeee
Q psy10165 67 ERGWSGGKLGGRSLGPPDPVGENTAKEIWAGVTGVSNAGKKRGRGRGPGKLTARDLNRGQIIGIDTFDGFDTRILEYKAV 146 (337)
Q Consensus 67 e~gW~g~~~~grsvgpp~~~~~~~~~~~~k~~~~~~~~~~~~~r~~~~~~~~~~~l~~~eiId~~~~~~f~~~VL~v~rV 146 (337)
++.|.|.++.||.|..- .+. |.||||+ +..+|+|.||||++ +++|+++||+++||
T Consensus 6 ~~~w~p~t~lg~lv~~~-~i~--s~e~i~~---------------------~~~~i~e~eivd~l-l~~l~e~vv~i~rV 60 (211)
T PRK04044 6 IEEWEPKTRLGRLVKEG-KIT--SIDEIFD---------------------SGLPIKEPEIVDVL-LPDLEDEVLDINMV 60 (211)
T ss_pred ccCccccchhhhhhhcC-Ccc--cHHHHHh---------------------cCCCcccchhhhhh-hccceeEEEEEEeE
Confidence 45699999999999977 554 8999999 78899999999965 57999999999999
Q ss_pred eeeecCCCceEEEEEEEEEeCCCCceeeecccchhHHHHHHHHHHHHccCcEEEecc---------CCcceeEeEEEEEc
Q psy10165 147 FCMKKNSGRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQKLIYVQRY---------KDHTVLHDFYTQFG 217 (337)
Q Consensus 147 ~kmT~~~GR~~rf~alVvVGNgnG~vG~G~GKa~ev~~AirkA~~~Ak~nli~V~r~---------~~~TIph~v~gk~g 217 (337)
+|||+ +||++||+|||||||+||++|||+|||+|+.+||++|+.+|++||++|+++ ++|||||++.|||+
T Consensus 61 ~kvtk-gGr~~sf~alVvVGn~~G~vG~G~GKa~ev~~Ai~kA~~~Akknli~V~r~~g~We~~~~~~~TI~h~v~gk~g 139 (211)
T PRK04044 61 QRMTD-SGRRVRFRVVVVVGNRDGYVGVGQGKAKQVGPAIRKAIRNAKLNIIKVRRGCGSWECGCGEPHSVPFKVTGKAG 139 (211)
T ss_pred Eeeec-CCcEEEEEEEEEEeCCCCeEeeeeeeccchHHHHHHHHHHHHhCeEEEEcccccccccCCCCCcCCeEEEEEEc
Confidence 99999 999999999999999999999999999999999999999999999999996 78999999999999
Q ss_pred eEEEEEEeCCCccceeechHHHHHHHHcCCCcceeeecCCC-ChhhHHHHHHHHHhc---CCCHHHHHHHhC
Q psy10165 218 KTKIFVEKKPEGTGLICHRIIQEICKAVGIKDIRAKVEGST-NPQAIVKAFFLGLMQ---QKSHQQLAEEQQ 285 (337)
Q Consensus 218 stkV~l~PaP~G~Glva~~~ir~Il~laGIkDv~aKv~Gst-n~~NvvkAtf~AL~~---~~t~~~iA~~rG 285 (337)
+++|+|+|||+|+||+|++.+++||++|||+||++|++||+ |++|++||||+||.+ +.+|++.++.+|
T Consensus 140 s~~V~l~Pap~GtGiiag~~vr~vlelaGIkDv~aK~~Gstrn~~N~vkAt~~AL~~~~~~~~p~~~~~~~~ 211 (211)
T PRK04044 140 SVEVTLKPAPRGLGLVAGDVAKKVLELAGIKDVWTRTFGETRTTVNFAKATFNALKNTYKVRTPPDWAEKRG 211 (211)
T ss_pred cEEEEEEECCCCCeEEECcHHHHHHHHcCcceEEEEccCCCCChhHHHHHHHHHHHHHHcccCHHHHHhhcC
Confidence 99999999999999999999999999999999999999997 999999999999995 668888887654
No 2
>PTZ00070 40S ribosomal protein S2; Provisional
Probab=100.00 E-value=6e-55 Score=408.29 Aligned_cols=187 Identities=21% Similarity=0.297 Sum_probs=178.1
Q ss_pred CCCCCCCCCCCCccCCCCCCCCCChhhhhhhccccccccccccCCCCCCCcccccccCcccccccccC-CCcceEEEEEe
Q psy10165 66 LERGWSGGKLGGRSLGPPDPVGENTAKEIWAGVTGVSNAGKKRGRGRGPGKLTARDLNRGQIIGIDTF-DGFDTRILEYK 144 (337)
Q Consensus 66 le~gW~g~~~~grsvgpp~~~~~~~~~~~~k~~~~~~~~~~~~~r~~~~~~~~~~~l~~~eiId~~~~-~~f~~~VL~v~ 144 (337)
-+..|.|.++.||.|..- .+. |+||||. ++.+|+|.||||+++. ++|+++||+|+
T Consensus 33 ~~~~W~P~TklGrlVk~g-ki~--s~eei~~---------------------~~lpikE~eIvd~ll~~~~L~eeVl~I~ 88 (257)
T PTZ00070 33 EEKEWVPVTKLGRLVKAG-KIT--SLEEIFL---------------------FSIPIKEYQIVDHFFAESKLKDEVMKIM 88 (257)
T ss_pred ccCceeeccchhhhhhcC-ccc--cHHHHHh---------------------cCCCccchhhHHHHccCccchheEEEEe
Confidence 466899999999999876 565 8999999 8999999999998775 89999999999
Q ss_pred eeeeeecCCCceEEEEEEEEEeCCCCceeeecccchhHHHHHHHHHHHHccCcEEEecc-------CCcceeEeEEEEEc
Q psy10165 145 AVFCMKKNSGRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQKLIYVQRY-------KDHTVLHDFYTQFG 217 (337)
Q Consensus 145 rV~kmT~~~GR~~rf~alVvVGNgnG~vG~G~GKa~ev~~AirkA~~~Ak~nli~V~r~-------~~~TIph~v~gk~g 217 (337)
+|||||+ +||++||+|||||||+||+||||+|||+|+.+||++|+.+|++||++|+|+ ++|||||+++|||+
T Consensus 89 rVqK~Tk-gGrr~rF~AlVVVGd~nG~VGlG~gKakEV~~AIrKAi~~AK~nii~V~rgyW~~~~g~~hTIp~~V~GK~G 167 (257)
T PTZ00070 89 PVQKQTS-AGQRTRFKAFVVVGDGNGHIGLGAKVAKEVATAIRGAIIAAKLNLVPVRRGYWGNKIGEPHTVPMKVTGKCG 167 (257)
T ss_pred eeEEEec-CCcEEEEEEEEEEeCCCCcEecceeechhHHHHHHHHHHHHHhCeEEEecccccccCCCCCCeeeeEEEEeC
Confidence 9999999 999999999999999999999999999999999999999999999999983 67999999999999
Q ss_pred eEEEEEEeCCCccceeechHHHHHHHHcCCCcceeeecCCC-ChhhHHHHHHHHHhcCCCH
Q psy10165 218 KTKIFVEKKPEGTGLICHRIIQEICKAVGIKDIRAKVEGST-NPQAIVKAFFLGLMQQKSH 277 (337)
Q Consensus 218 stkV~l~PaP~G~Glva~~~ir~Il~laGIkDv~aKv~Gst-n~~NvvkAtf~AL~~~~t~ 277 (337)
|++|+|+|||+|+||+|++++++||++|||+||++|+.||+ |++|++||||+||.+++++
T Consensus 168 Sv~V~L~PAP~GtGivAg~~vk~VLelAGIkDv~tks~GsTrt~~N~aKATf~AL~~t~~~ 228 (257)
T PTZ00070 168 SVRVRLVPAPRGTGIVAAPTPKKILEFAGVEDVFTSSRGKTRTRGNFLKATFYALRKTYGF 228 (257)
T ss_pred eEEEEEEeCCCCccEEeCcHHHHHHHHcCccceeeecccCCCChHHHHHHHHHHHHHHhcc
Confidence 99999999999999999999999999999999999999998 9999999999999987753
No 3
>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=1.3e-54 Score=398.16 Aligned_cols=183 Identities=23% Similarity=0.370 Sum_probs=175.0
Q ss_pred CCCCCCCCCCCccCCCCCCCCCChhhhhhhccccccccccccCCCCCCCcccccccCcccccccccCCCc-ceEEEEEee
Q psy10165 67 ERGWSGGKLGGRSLGPPDPVGENTAKEIWAGVTGVSNAGKKRGRGRGPGKLTARDLNRGQIIGIDTFDGF-DTRILEYKA 145 (337)
Q Consensus 67 e~gW~g~~~~grsvgpp~~~~~~~~~~~~k~~~~~~~~~~~~~r~~~~~~~~~~~l~~~eiId~~~~~~f-~~~VL~v~r 145 (337)
+..|.|.++.||.|..- .+. |+||||. ++.+|+|.||||+++ ++| +++||+|++
T Consensus 5 ~~~w~p~t~lgrlV~~g-~i~--s~~ei~~---------------------~~~~i~E~eivd~ll-~~l~~e~vl~I~r 59 (212)
T TIGR01020 5 LEEWVPRTKLGRLVKEG-KIK--SIDEIFL---------------------RNLPIKEPEIVDYLL-PDLNEEEVLDVSL 59 (212)
T ss_pred ccCeeecchhhhhhhcC-Ccc--cHHHHHH---------------------cCCCccchhhHHHHh-hhcCcceEEEEEe
Confidence 45699999999999876 554 8999999 899999999999765 599 889999999
Q ss_pred eeeeecCCCceEEEEEEEEEeCCCCceeeecccchhHHHHHHHHHHHHccCcEEEec---------cCCcceeEeEEEEE
Q psy10165 146 VFCMKKNSGRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQKLIYVQR---------YKDHTVLHDFYTQF 216 (337)
Q Consensus 146 V~kmT~~~GR~~rf~alVvVGNgnG~vG~G~GKa~ev~~AirkA~~~Ak~nli~V~r---------~~~~TIph~v~gk~ 216 (337)
|||||+ +||++||+|||||||+||++|||+|||+|+.+||++|+.+|++||++|+| +++|||||++.|||
T Consensus 60 V~K~tk-gGr~~~F~alVvVGn~~G~vG~G~GKa~ev~~AI~kA~~~Ak~n~i~V~rg~g~w~~~~~~~hTIp~~v~Gk~ 138 (212)
T TIGR01020 60 VQRMTD-SGRRTRFRAFVVVGNRDGYVGLGIGKAKEVAPAIRKAIINAKLNIIPVRRGCGSWECGCGRPHSVPFKVTGKC 138 (212)
T ss_pred eEEEec-CCcEEEEEEEEEEeCCCCeEeeceeecchHHHHHHHHHHHHHhCEEEEecccccccccCCCCCcEeEEEEEEE
Confidence 999999 99999999999999999999999999999999999999999999999999 47999999999999
Q ss_pred ceEEEEEEeCCCccceeechHHHHHHHHcCCCcceeeecCCC-ChhhHHHHHHHHHhcCC
Q psy10165 217 GKTKIFVEKKPEGTGLICHRIIQEICKAVGIKDIRAKVEGST-NPQAIVKAFFLGLMQQK 275 (337)
Q Consensus 217 gstkV~l~PaP~G~Glva~~~ir~Il~laGIkDv~aKv~Gst-n~~NvvkAtf~AL~~~~ 275 (337)
||++|+|+|||+|+||+|++++++||++|||+||++|++||+ |++|++||||+||.+++
T Consensus 139 gs~~V~L~PAP~GtGliag~~~r~ilelAGIkDv~tk~~Gstrn~~N~~kAtf~AL~~~~ 198 (212)
T TIGR01020 139 GSVRVRLIPAPRGLGLVAGDVAKKVLRLAGIDDVWTQTRGETRTTVNFAKATFDALKKTY 198 (212)
T ss_pred ccEEEEEEeCCCCCceecCcHHHHHHHHcCccceeeeccCCCCChhHHHHHHHHHHHhcc
Confidence 999999999999999999999999999999999999999998 99999999999999887
No 4
>PRK00550 rpsE 30S ribosomal protein S5; Validated
Probab=100.00 E-value=1.5e-53 Score=380.35 Aligned_cols=157 Identities=31% Similarity=0.479 Sum_probs=154.8
Q ss_pred CCcceEEEEEeeeeeeecCCCceEEEEEEEEEeCCCCceeeecccchhHHHHHHHHHHHHccCcEEEeccCCcceeEeEE
Q psy10165 134 DGFDTRILEYKAVFCMKKNSGRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQKLIYVQRYKDHTVLHDFY 213 (337)
Q Consensus 134 ~~f~~~VL~v~rV~kmT~~~GR~~rf~alVvVGNgnG~vG~G~GKa~ev~~AirkA~~~Ak~nli~V~r~~~~TIph~v~ 213 (337)
++|+++||++++|+|||+ +||+++|+|||+|||+||++|||+|||+|+.+||++|+.+|++||++|+++ +|||||++.
T Consensus 11 ~~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 11 LELEEKVVAINRVTKVVK-GGRRFSFSALVVVGDGKGRVGFGYGKAREVPEAIRKAVEDAKKNMIKVPLV-GGTIPHEVI 88 (168)
T ss_pred CCceEEEEEEeeeEEEec-CCcEEEEEEEEEEECCCCeEeeeeeecchHHHHHHHHHHHHHhCEEEEecC-CCccceeEE
Confidence 489999999999999999 999999999999999999999999999999999999999999999999999 999999999
Q ss_pred EEEceEEEEEEeCCCccceeechHHHHHHHHcCCCcceeeecCCCChhhHHHHHHHHHhcCCCHHHHHHHhCCchhhhc
Q psy10165 214 TQFGKTKIFVEKKPEGTGLICHRIIQEICKAVGIKDIRAKVEGSTNPQAIVKAFFLGLMQQKSHQQLAEEQQLHLVEFS 292 (337)
Q Consensus 214 gk~gstkV~l~PaP~G~Glva~~~ir~Il~laGIkDv~aKv~Gstn~~NvvkAtf~AL~~~~t~~~iA~~rG~~vve~~ 292 (337)
+||++++|+|+|||+|+||+|++.++.||++|||+||++|++||+||+|++||||+||.+++||+|+|+.||++++|+.
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 9999999999999999999999999999999999999999999999999999999999999999999999999999975
No 5
>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=3.3e-53 Score=373.53 Aligned_cols=153 Identities=33% Similarity=0.489 Sum_probs=150.6
Q ss_pred CcceEEEEEeeeeeeecCCCceEEEEEEEEEeCCCCceeeecccchhHHHHHHHHHHHHccCcEEEeccCCcceeEeEEE
Q psy10165 135 GFDTRILEYKAVFCMKKNSGRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQKLIYVQRYKDHTVLHDFYT 214 (337)
Q Consensus 135 ~f~~~VL~v~rV~kmT~~~GR~~rf~alVvVGNgnG~vG~G~GKa~ev~~AirkA~~~Ak~nli~V~r~~~~TIph~v~g 214 (337)
+|+++||+|+||+|||+ +||++||+|||+|||+||++|||+|||+|+.+|+++|+.+|++||++|+++++ ||||++.+
T Consensus 1 ~l~e~vl~i~rv~k~tk-gGr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~kA~~~Ak~nl~~V~~~~~-Ti~~~v~g 78 (154)
T TIGR01021 1 ELEERLIAVNRVSKVVK-GGRRFSFSALVVVGDGKGRVGFGFGKAKEVPDAIKKAVEKARKNLINVPLTKG-TIPHEVIG 78 (154)
T ss_pred CceeEEEEEeeeeEEec-CCcEEEEEEEEEEECCCCeEeeeeeecchHHHHHHHHHHHHHhCeEEEecCCC-ccceEEEE
Confidence 48999999999999999 99999999999999999999999999999999999999999999999999988 99999999
Q ss_pred EEceEEEEEEeCCCccceeechHHHHHHHHcCCCcceeeecCCCChhhHHHHHHHHHhcCCCHHHHHHHhCCchh
Q psy10165 215 QFGKTKIFVEKKPEGTGLICHRIIQEICKAVGIKDIRAKVEGSTNPQAIVKAFFLGLMQQKSHQQLAEEQQLHLV 289 (337)
Q Consensus 215 k~gstkV~l~PaP~G~Glva~~~ir~Il~laGIkDv~aKv~Gstn~~NvvkAtf~AL~~~~t~~~iA~~rG~~vv 289 (337)
||++++|+|+|||+|+||+|++.++.||++|||+||++|++||+||+|++||||+||.+++||+|+|++||+++-
T Consensus 79 k~gs~~V~l~Pap~G~Gi~a~~~~~~il~laGI~Dv~~k~~Gs~n~~n~vkAt~~aL~~~~s~~~ia~~rG~~~~ 153 (154)
T TIGR01021 79 VSGAAKVLLKPASPGTGVIAGGAVRAILELAGVKDILAKSLGSNNPINVVRATFDALLKLKSPEDVAELRGKSVE 153 (154)
T ss_pred EECcEEEEEEECCCCCceEeCcHHHHHHHHcCcceEEEEccCCCChHHHHHHHHHHHHcCCCHHHHHHHcCCCcc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999974
No 6
>COG0098 RpsE Ribosomal protein S5 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4e-53 Score=378.94 Aligned_cols=159 Identities=30% Similarity=0.486 Sum_probs=155.8
Q ss_pred CCCcceEEEEEeeeeeeecCCCceEEEEEEEEEeCCCCceeeecccchhHHHHHHHHHHHHccCcEEEeccCCcceeEeE
Q psy10165 133 FDGFDTRILEYKAVFCMKKNSGRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQKLIYVQRYKDHTVLHDF 212 (337)
Q Consensus 133 ~~~f~~~VL~v~rV~kmT~~~GR~~rf~alVvVGNgnG~vG~G~GKa~ev~~AirkA~~~Ak~nli~V~r~~~~TIph~v 212 (337)
.+.|.++||+|+||+|||+ +||++||+|||||||+||+||||.|||+|++.||+||+..|++||++|+++++|||||++
T Consensus 21 ~~~l~e~vv~inrV~K~~k-gGRr~~F~alvVVGd~~G~VG~G~GKA~EV~~AIrKAi~~Ak~nii~V~~~~~~Tiph~v 99 (181)
T COG0098 21 VDELLEKVVDINRVSKVVK-GGRRFRFSALVVVGDRNGRVGFGIGKAKEVPEAIRKAIEDAKKNIIEVPRGNGHTIPHEV 99 (181)
T ss_pred hhhcceeeeEEEEEEEeec-CceEEEEEEEEEEeCCCCeEeeeecchhhhHHHHHHHHHHHHhCeEEEecCCCceeeeEE
Confidence 4578899999999999999 999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEceEEEEEEeCCCccceeechHHHHHHHHcCCCcceeeecCCCChhhHHHHHHHHHhcCCCHHHHHHHhCCchhhhc
Q psy10165 213 YTQFGKTKIFVEKKPEGTGLICHRIIQEICKAVGIKDIRAKVEGSTNPQAIVKAFFLGLMQQKSHQQLAEEQQLHLVEFS 292 (337)
Q Consensus 213 ~gk~gstkV~l~PaP~G~Glva~~~ir~Il~laGIkDv~aKv~Gstn~~NvvkAtf~AL~~~~t~~~iA~~rG~~vve~~ 292 (337)
.|+|++++|.|+|||+|+||+|++++++|||+|||+|||+|++||+|++|++||||+||.++.+|+++|.+||+.+.++.
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 99999999999999999999999999999999999999999999999999999999999999999999999999998875
No 7
>KOG2646|consensus
Probab=100.00 E-value=9.4e-54 Score=414.23 Aligned_cols=269 Identities=31% Similarity=0.439 Sum_probs=247.9
Q ss_pred cccceEeccccccccCCCCCcccccCcee--eecccCCCChhHHHHHHHhhhhhhccccCCCCCCCCCCCCCCCCCccCC
Q psy10165 4 IVQGWIWNLGKINIQWPGLSAPVIRGREL--VQQTRLPPDPDREAKLIALRDKQFQGKYRKTPPLERGWSGGKLGGRSLG 81 (337)
Q Consensus 4 ~~~~~~~~~g~~~~~~pgl~~p~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~ple~gW~g~~~~grsvg 81 (337)
.+++|..+.+..+|+|+ .|+...+++ +.|+..+.++.++.+|++.|.+|. .+++.++||+|..|.+.++|
T Consensus 97 ~i~aq~ede~~e~fi~~---~pL~~~g~~k~~~ers~~~ke~~~~dld~~r~~~D-----~~~k~~~G~~~~k~~~~k~g 168 (396)
T KOG2646|consen 97 DIDAQDEDEYREPFIWK---QPLKDDGELKRIAERSDSGKENDEIDLDEERKKED-----IFSKKERGHSGLKWTDTKLG 168 (396)
T ss_pred hhhhhhhhhhhhhcccC---CccchhhhhhhhhcccCcccccccchhhhhhhhhh-----ccCchhcCCCcccccccccC
Confidence 35789999999999999 999998887 888999999999999999999998 45778999999999999999
Q ss_pred CCCCCCCChhhhhhhccccccccccccCCCCCCCcccccccCcccccccccCCCcceEEEEE-ee-eeeeecCCCceEEE
Q psy10165 82 PPDPVGENTAKEIWAGVTGVSNAGKKRGRGRGPGKLTARDLNRGQIIGIDTFDGFDTRILEY-KA-VFCMKKNSGRYRTV 159 (337)
Q Consensus 82 pp~~~~~~~~~~~~k~~~~~~~~~~~~~r~~~~~~~~~~~l~~~eiId~~~~~~f~~~VL~v-~r-V~kmT~~~GR~~rf 159 (337)
+|++... . +.+.+|+++.|++ ++ |.+|++ .|++-++
T Consensus 169 ~~~e~~~-~----------------------------------------~n~~Dfe~r~l~lvrr~~~~~~r-~Gki~s~ 206 (396)
T KOG2646|consen 169 LPDEAFR-G----------------------------------------MNYLDFELRHLELVRRRVENQNR-KGKIASM 206 (396)
T ss_pred CCCcccc-C----------------------------------------CCchhhhHHHHHHHHhhhhcccc-ccceeeE
Confidence 9988643 1 5677889999988 44 556665 9999999
Q ss_pred EEEEEEeCCCCceeeecccch-hHHHHHHHHHHHHccCcEEEeccCCcceeEeEEEEEceEEEEEEeCCCccceeechHH
Q psy10165 160 STLVVTGNGQGLAGFALGKSV-EGRASMRNAKNRAGQKLIYVQRYKDHTVLHDFYTQFGKTKIFVEKKPEGTGLICHRII 238 (337)
Q Consensus 160 ~alVvVGNgnG~vG~G~GKa~-ev~~AirkA~~~Ak~nli~V~r~~~~TIph~v~gk~gstkV~l~PaP~G~Glva~~~i 238 (337)
+|||||||+||++|||+|||. +...|+.+|+.+|.+||.+|+||++|||+||+..+|..++++|+.+|+|+||.||+++
T Consensus 207 ~~LVvvGn~nGaaG~~eGKa~~~~s~A~~ka~~rAv~~l~~ieRyE~rTiygDi~~r~~~~~l~mk~rp~GfGLrcn~il 286 (396)
T KOG2646|consen 207 YALVVVGNGNGAAGLGEGKAADPNSPAIYKAIGRAVRNLGYIERYERRTIYGDIDDRFHEVRLDMKSRPDGFGLRCNPIL 286 (396)
T ss_pred EEEEEEecCCcceeeccccCcCccCHHHHHHHHHHHhhcCccccccCccccccchhhhhhhhhhhhhCCCcccccccHHH
Confidence 999999999999999999999 7889999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCCCcceeeecCCCChhhHHHHHHHHHhcCCCHHHHHHHhCCchhhhccccCCcceeeecCCC-cCCCCCC---
Q psy10165 239 QEICKAVGIKDIRAKVEGSTNPQAIVKAFFLGLMQQKSHQQLAEEQQLHLVEFSEENDNYPTIVASPST-CKKDSSK--- 314 (337)
Q Consensus 239 r~Il~laGIkDv~aKv~Gstn~~NvvkAtf~AL~~~~t~~~iA~~rG~~vve~~~e~~~~p~vvasp~~-~~~~~~~--- 314 (337)
.+||++|||+|+++|+.||+|.+|+++|+|+||..|+||||+|.++|+||||++.++.++|++||||-+ .++++|.
T Consensus 287 ~kIC~~~GIKDis~kv~GsrN~m~i~k~~~e~l~~qet~qqlA~rkG~hvVdVr~e~~~~t~~vaspig~~~k~~et~~~ 366 (396)
T KOG2646|consen 287 IKICECAGIKDISGKVKGSRNEMNITKAAFEALALQETHQQLAYRKGLHVVDVRGEVYRLTGNVASPIGYAKKKAETGQS 366 (396)
T ss_pred HHHHHHhccccccceeeccchHHHHHHHHHHHHhhhhhhHHHHHhcCCeEEEeccceeecccceecccchhhcCCccccc
Confidence 999999999999999999999999999999999999999999999999999999999999999999977 7887773
Q ss_pred ----CCChhhhh
Q psy10165 315 ----APDFTEVS 322 (337)
Q Consensus 315 ----~~~~~~~~ 322 (337)
.+||++|+
T Consensus 367 ~p~vk~~~e~~~ 378 (396)
T KOG2646|consen 367 LPYVKRHEEHIA 378 (396)
T ss_pred ccccccchhhhh
Confidence 27777754
No 8
>CHL00138 rps5 ribosomal protein S5; Validated
Probab=100.00 E-value=2.3e-42 Score=301.30 Aligned_cols=123 Identities=26% Similarity=0.447 Sum_probs=121.2
Q ss_pred CCCcceEEEEEeeeeeeecCCCceEEEEEEEEEeCCCCceeeecccchhHHHHHHHHHHHHccCcEEEeccCCcceeEeE
Q psy10165 133 FDGFDTRILEYKAVFCMKKNSGRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQKLIYVQRYKDHTVLHDF 212 (337)
Q Consensus 133 ~~~f~~~VL~v~rV~kmT~~~GR~~rf~alVvVGNgnG~vG~G~GKa~ev~~AirkA~~~Ak~nli~V~r~~~~TIph~v 212 (337)
.++|+++||+++||++||+ +||+++|+|||+|||+||++|||+|||.|+.+|+++|..+|++||++|+++++|||||++
T Consensus 21 ~~~l~ekvl~i~rV~k~tk-gGR~~~f~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknl~~V~~~~~~TI~~~v 99 (143)
T CHL00138 21 ENKWEERVIQIKRVSKVVK-GGKKLSFRAIVVIGNENGWVGVGVGKADDVQNAVKKAVTDAKKNLITIPLTKSNSIPHNI 99 (143)
T ss_pred CCCceEEEEEEeeeeEEec-CCcEEEEEEEEEEECCCCeEEEeeEecchHHHHHHHHHHHHHhCeEEEEcCCCCeEeeEE
Confidence 4789999999999999999 999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEceEEEEEEeCCCccceeechHHHHHHHHcCCCcceeeecC
Q psy10165 213 YTQFGKTKIFVEKKPEGTGLICHRIIQEICKAVGIKDIRAKVEG 256 (337)
Q Consensus 213 ~gk~gstkV~l~PaP~G~Glva~~~ir~Il~laGIkDv~aKv~G 256 (337)
.++|++++|+|+|||+|+||+|++.+++||++|||+||++|+.|
T Consensus 100 ~gk~gs~~V~l~Pap~G~Gi~a~~~i~~vlelaGI~Dv~aK~~G 143 (143)
T CHL00138 100 TGIFGAAKVILRPSAPGSGVIAGGSVRIVLELAGIKNILAKQLG 143 (143)
T ss_pred EEEEeeEEEEEEECCCCCcEEECcHHHHHHHHcCcceeEeeecC
Confidence 99999999999999999999999999999999999999999987
No 9
>KOG0877|consensus
Probab=100.00 E-value=4.8e-41 Score=304.68 Aligned_cols=189 Identities=22% Similarity=0.276 Sum_probs=179.7
Q ss_pred CCCCCCCCCCCCCCccCCCCCCCCCChhhhhhhccccccccccccCCCCCCCcccccccCcccccccccCCCcceEEEEE
Q psy10165 64 PPLERGWSGGKLGGRSLGPPDPVGENTAKEIWAGVTGVSNAGKKRGRGRGPGKLTARDLNRGQIIGIDTFDGFDTRILEY 143 (337)
Q Consensus 64 ~ple~gW~g~~~~grsvgpp~~~~~~~~~~~~k~~~~~~~~~~~~~r~~~~~~~~~~~l~~~eiId~~~~~~f~~~VL~v 143 (337)
.|-|..|.+.+..|+.+.-- .+. +.+||+. ++.+++|.||||+++...|+++||+|
T Consensus 3 ~~~~~~~~p~t~lG~lv~~~-ki~--sleeiyl---------------------~slpike~eiid~~lg~slkdeVLkI 58 (213)
T KOG0877|consen 3 APEEKEWMPVTKLGRLVKDM-KIK--SLEEIYL---------------------FSLPIKESEIIDFFLGASLKDEVLKI 58 (213)
T ss_pred CCccCcCCCcccccccchhc-hhh--hhhhhhc---------------------cCccccchhhhhhhhccchHhhhhee
Confidence 45688999999999999876 555 7888888 89999999999999999999999999
Q ss_pred eeeeeeecCCCceEEEEEEEEEeCCCCceeeecccchhHHHHHHHHHHHHccCcEEEecc-------CCcceeEeEEEEE
Q psy10165 144 KAVFCMKKNSGRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQKLIYVQRY-------KDHTVLHDFYTQF 216 (337)
Q Consensus 144 ~rV~kmT~~~GR~~rf~alVvVGNgnG~vG~G~GKa~ev~~AirkA~~~Ak~nli~V~r~-------~~~TIph~v~gk~ 216 (337)
++|+|||+ +|+++||+|+|+|||+||+||+|+.+++|+++||++|+..|++++++|+|+ .+||+|+++.|+|
T Consensus 59 mpVqKqtr-AGQrtRfKAfVaigD~~ghVGlgvk~sKeva~airgaiilaklsivpvrrgyw~~~~g~pHt~~~kvtg~~ 137 (213)
T KOG0877|consen 59 MPVQKQTR-AGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGDC 137 (213)
T ss_pred eecccccc-cccccceEEEEEEeecCCceeeeeeehHHHHHHHhHHHhhhheeeeeeeccccccccCCCccccCcccccC
Confidence 99999999 999999999999999999999999999999999999999999999999997 6999999999999
Q ss_pred ceEEEEEEeCCCccceeechHHHHHHHHcCCCcceeeecCCC-ChhhHHHHHHHHHhcCCCH
Q psy10165 217 GKTKIFVEKKPEGTGLICHRIIQEICKAVGIKDIRAKVEGST-NPQAIVKAFFLGLMQQKSH 277 (337)
Q Consensus 217 gstkV~l~PaP~G~Glva~~~ir~Il~laGIkDv~aKv~Gst-n~~NvvkAtf~AL~~~~t~ 277 (337)
+++.|.+.|+|+|+||++.++.+++|++|||+|||+++.||| ++.|++||+|.|+++++++
T Consensus 138 ~svlv~l~papRgtGivs~p~~kkll~mAGi~d~~t~~~G~t~tl~n~~ka~~~a~~~ty~~ 199 (213)
T KOG0877|consen 138 GSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSY 199 (213)
T ss_pred CcceEEEeecCCCCceeeccccHHHHHhccccccchhhcccchhhccHHHHHHHHHHhhhhh
Confidence 999999999999999999999999999999999999999999 9999999999999987764
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=99.94 E-value=5.2e-27 Score=184.21 Aligned_cols=74 Identities=41% Similarity=0.653 Sum_probs=72.7
Q ss_pred EEEEEceEEEEEEeCCCccceeechHHHHHHHHcCCCcceeeecCCCChhhHHHHHHHHHhcCCCHHHHHHHhC
Q psy10165 212 FYTQFGKTKIFVEKKPEGTGLICHRIIQEICKAVGIKDIRAKVEGSTNPQAIVKAFFLGLMQQKSHQQLAEEQQ 285 (337)
Q Consensus 212 v~gk~gstkV~l~PaP~G~Glva~~~ir~Il~laGIkDv~aKv~Gstn~~NvvkAtf~AL~~~~t~~~iA~~rG 285 (337)
|.+||++++|+|+|+|+|+||+||+.+++||+++||+||++|++||+|++|++||||+||.+++|++++|++||
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 68999999999999999999999999999999999999999999999999999999999999999999999997
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=99.88 E-value=6.6e-23 Score=158.35 Aligned_cols=67 Identities=45% Similarity=0.713 Sum_probs=64.6
Q ss_pred CcceEEEEEeeeeeeecCCCceEEEEEEEEEeCCCCceeeecccchhHHHHHHHHHHHHccCcEEEec
Q psy10165 135 GFDTRILEYKAVFCMKKNSGRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQKLIYVQR 202 (337)
Q Consensus 135 ~f~~~VL~v~rV~kmT~~~GR~~rf~alVvVGNgnG~vG~G~GKa~ev~~AirkA~~~Ak~nli~V~r 202 (337)
+|+++||++++|++||+ +||+++|+|||+|||+||++|||+|||.|+.+|+++|..+|++||++|+|
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 DLEEKVLEVKRVSKMTK-GGRIFSFRALVVVGNGNGLVGFGVGKAKEVPDAIRKAKRKAKKNLIYVPR 67 (67)
T ss_dssp SHEEEEEEEEEEEEEET-TEEEEEEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHHHCSEEE-SC
T ss_pred CceEEEEEEEEEEEEec-CCceeEEEEEEEEecCCCcEecCcccchhHHHHHHHHHHHHHhCCEECcC
Confidence 58999999999999999 99999999999999999999999999999999999999999999999986
No 12
>smart00358 DSRM Double-stranded RNA binding motif.
Probab=39.63 E-value=73 Score=22.65 Aligned_cols=39 Identities=21% Similarity=0.210 Sum_probs=25.5
Q ss_pred ceEEEEEEEEEeCCCCceeeecccchhHHHHHHHHHHHHccCc
Q psy10165 155 RYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQKL 197 (337)
Q Consensus 155 R~~rf~alVvVGNgnG~vG~G~GKa~ev~~AirkA~~~Ak~nl 197 (337)
....|.+-|.+++. .++-|.|.+ -.+|-+.|-..|...|
T Consensus 28 ~~~~f~~~v~i~~~--~~~~g~g~s--Kk~Ak~~AA~~al~~L 66 (67)
T smart00358 28 HAPRFTVTVKVGGE--YTGEGEGSS--KKEAKQRAAEAALRSL 66 (67)
T ss_pred CCCcEEEEEEECCE--EEEEeccCC--HHHHHHHHHHHHHHhc
Confidence 34578888888543 566666555 4677778777776554
No 13
>PF14493 HTH_40: Helix-turn-helix domain
Probab=37.98 E-value=39 Score=26.92 Aligned_cols=30 Identities=10% Similarity=0.032 Sum_probs=24.3
Q ss_pred HHHHHHHHHhcCCCHHHHHHHhCCchhhhc
Q psy10165 263 IVKAFFLGLMQQKSHQQLAEEQQLHLVEFS 292 (337)
Q Consensus 263 vvkAtf~AL~~~~t~~~iA~~rG~~vve~~ 292 (337)
...-|++-+.+-.|.++||+.||++.-.+.
T Consensus 2 t~~~T~~l~~~G~si~eIA~~R~L~~sTI~ 31 (91)
T PF14493_consen 2 TAQITYELFQKGLSIEEIAKIRGLKESTIY 31 (91)
T ss_pred HHHHHHHHHHcCCCHHHHHHHcCCCHHHHH
Confidence 356688888999999999999999864443
No 14
>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=37.69 E-value=1.1e+02 Score=21.53 Aligned_cols=39 Identities=23% Similarity=0.256 Sum_probs=26.1
Q ss_pred CceEEEEEEEEEeCCCCceeeecccchhHHHHHHHHHHHHccC
Q psy10165 154 GRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQK 196 (337)
Q Consensus 154 GR~~rf~alVvVGNgnG~vG~G~GKa~ev~~AirkA~~~Ak~n 196 (337)
+....|.+-|.+++ -..+.|.|++ -.+|-+.|-..|...
T Consensus 29 ~~~~~f~~~v~i~~--~~~~~g~g~s--Kk~Ak~~AA~~al~~ 67 (68)
T cd00048 29 DHAPRFTVEVTVGG--KITGEGEGSS--KKEAKQNAAEAALRK 67 (68)
T ss_pred CCCCeEEEEEEECC--EEEEEeecCC--HHHHHHHHHHHHHHh
Confidence 33568888888866 3666666654 467777777766543
No 15
>PF01990 ATP-synt_F: ATP synthase (F/14-kDa) subunit; InterPro: IPR008218 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents subunit F found in the V1 complex of V-ATPases (both eukaryotic and bacterial), as well as in the A1 complex of A-ATPases. Subunit F is a 16 kDa protein that is required for the assembly and activity of V-ATPase, and has a potential role in the differential targeting and regulation of the enzyme for specific organelles. This subunit is not necessary for the rotation of the ATPase V1 rotor, but it does promote catalysis []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain; PDB: 2D00_E 3A5C_P 3J0J_H 3A5D_H 2OV6_A 2QAI_B 3AON_B 2I4R_A.
Probab=34.68 E-value=33 Score=27.56 Aligned_cols=71 Identities=25% Similarity=0.301 Sum_probs=48.8
Q ss_pred eeechHHHHHHHHcCCCcceeeecCCCChhhHHHHHHHHHhc-CC----CHHHHHHHhCCchhhhccccCCcceeeecCC
Q psy10165 232 LICHRIIQEICKAVGIKDIRAKVEGSTNPQAIVKAFFLGLMQ-QK----SHQQLAEEQQLHLVEFSEENDNYPTIVASPS 306 (337)
Q Consensus 232 lva~~~ir~Il~laGIkDv~aKv~Gstn~~NvvkAtf~AL~~-~~----t~~~iA~~rG~~vve~~~e~~~~p~vvasp~ 306 (337)
+++.+-.-.-+.|+|+..+++. +++.++..++-+.+.. .. --+++++.-...+-+++. ...+|.||.=|+
T Consensus 3 vIGd~~~v~gFrLaGv~~~~~~----~~~ee~~~~l~~l~~~~~~gIIii~e~~~~~~~~~l~~~~~-~~~~P~iv~IP~ 77 (95)
T PF01990_consen 3 VIGDRDTVLGFRLAGVEGVYVN----TDPEEAEEALKELLKDEDVGIIIITEDLAEKIRDELDEYRE-ESSLPLIVEIPS 77 (95)
T ss_dssp EEE-HHHHHHHHHTTSEEEEES----HSHHHHHHHHHHHHHHTTEEEEEEEHHHHTTHHHHHHHHHH-TSSSSEEEEEST
T ss_pred EEeCHHHHHHHHHcCCCCccCC----CCHHHHHHHHHHHhcCCCccEEEeeHHHHHHHHHHHHHHHh-ccCCceEEEcCC
Confidence 4566667778999999998876 6788888777776632 11 235566555555555543 349999999996
Q ss_pred C
Q psy10165 307 T 307 (337)
Q Consensus 307 ~ 307 (337)
.
T Consensus 78 ~ 78 (95)
T PF01990_consen 78 K 78 (95)
T ss_dssp T
T ss_pred C
Confidence 4
No 16
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.18 E-value=69 Score=28.20 Aligned_cols=57 Identities=16% Similarity=0.250 Sum_probs=40.0
Q ss_pred eechHHHHHHHHcCCCcceeeecCCCChhhHHH----HHHHHHhcCCCHHHHHHHhCCchh
Q psy10165 233 ICHRIIQEICKAVGIKDIRAKVEGSTNPQAIVK----AFFLGLMQQKSHQQLAEEQQLHLV 289 (337)
Q Consensus 233 va~~~ir~Il~laGIkDv~aKv~Gstn~~Nvvk----Atf~AL~~~~t~~~iA~~rG~~vv 289 (337)
..+..+.+.++-+||+.+-.|..|.--|-+.-+ -.-+-|.+-.+|.+|++..|..+-
T Consensus 64 k~skkvlkaleq~gI~vIPvk~KgrGrprkyd~~t~~~i~emlr~gk~preIsk~lGIpir 124 (139)
T COG1710 64 KVSKKVLKALEQMGIKVIPVKLKGRGRPRKYDRNTLLRIREMLRNGKTPREISKDLGIPIR 124 (139)
T ss_pred HHHHHHHHHHHhCCceEeeeeecCCCCCcccchhHHHHHHHHHHcCCCHHHHHHhhCCchh
Confidence 344444456677799999988777433444333 334677889999999999998764
No 17
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=33.98 E-value=95 Score=31.37 Aligned_cols=131 Identities=14% Similarity=0.131 Sum_probs=89.8
Q ss_pred CCCceeeecccchhHHHHHHHHHHHHccCcEEEeccCCc----ceeEeE---EEEEceEEEEEEeCCCcc----ceeech
Q psy10165 168 GQGLAGFALGKSVEGRASMRNAKNRAGQKLIYVQRYKDH----TVLHDF---YTQFGKTKIFVEKKPEGT----GLICHR 236 (337)
Q Consensus 168 gnG~vG~G~GKa~ev~~AirkA~~~Ak~nli~V~r~~~~----TIph~v---~gk~gstkV~l~PaP~G~----Glva~~ 236 (337)
-+|..-+|-...--..+++.+|.+..-.+..+|--...| -||..+ ..++-...+...|.|.|. +=.-+.
T Consensus 29 psG~~HIG~~~e~i~~D~i~R~lr~~G~~v~~v~~~Dd~d~lrKvp~~l~~~~~~~~G~pi~~ip~p~g~~~~~~d~~~~ 108 (353)
T cd00674 29 PSGHIHIGNFREVITADLVARALRDLGFEVRLIYSWDDYDRLRKVPPNVPESYEQYIGMPLSSVPDPFGCCESYAEHFER 108 (353)
T ss_pred CCCCcccCccHHHHHHHHHHHHHHHcCCCEEEEEEEcCCCcccccccchhhHHHHhcCccchhchhhcCCCHHHHHHHHH
Confidence 577777777776667789999999988898888777666 333322 345567888899999862 112234
Q ss_pred HHHHHHHHcCCCcceeeecCCC-Chh--hHHHHHHHHHhcCCCHHHHHHH-hCCchhhhccccCCcceeeecCC
Q psy10165 237 IIQEICKAVGIKDIRAKVEGST-NPQ--AIVKAFFLGLMQQKSHQQLAEE-QQLHLVEFSEENDNYPTIVASPS 306 (337)
Q Consensus 237 ~ir~Il~laGIkDv~aKv~Gst-n~~--NvvkAtf~AL~~~~t~~~iA~~-rG~~vve~~~e~~~~p~vvasp~ 306 (337)
..+.++..+||+- -...+| ... -+..+++.+|.+..-..+|-+. +|.. .+.+++|...-+|.
T Consensus 109 ~f~~~l~~lgi~~---d~~~~T~~y~~g~~~~~i~~~L~~~~~I~~i~~~~~~~~-----~~~~~~P~~p~c~~ 174 (353)
T cd00674 109 PFEESLEKLGIEV---EFISQSQMYKSGLYDENILIALEKRDEIMAILNEYRGRE-----LQETWYPFMPYCEK 174 (353)
T ss_pred HHHHHHHHcCCee---eeeecCCchhhchHHHHHHHHHHHCChHHHHHHHhcCCc-----cCCCceeeeeecCC
Confidence 6778888889863 244445 333 4788899999988887777644 4442 23566666666664
No 18
>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=32.88 E-value=1.8e+02 Score=20.70 Aligned_cols=40 Identities=23% Similarity=0.113 Sum_probs=26.0
Q ss_pred CCceEEEEEEEEEeCCCCceeeecccchhHHHHHHHHHHHHccC
Q psy10165 153 SGRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQK 196 (337)
Q Consensus 153 ~GR~~rf~alVvVGNgnG~vG~G~GKa~ev~~AirkA~~~Ak~n 196 (337)
.+....|.+-|.+++ =.+|.|.|++ -..|-+.|-..|.+.
T Consensus 27 ~~~~~~f~~~~~i~~--~~~~~g~g~s--Kk~Ak~~AA~~al~~ 66 (67)
T PF00035_consen 27 SHHRPRFICTVYIDG--KEYGEGEGSS--KKEAKQQAAKKALQK 66 (67)
T ss_dssp SSSSEEEEEEEEETT--EEEEEEEESS--HHHHHHHHHHHHHHH
T ss_pred CCCCceEEEEEEECC--EEEeEeccCC--HHHHHHHHHHHHHHh
Confidence 444458888888844 3466666654 467777777777654
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=29.09 E-value=84 Score=29.94 Aligned_cols=39 Identities=15% Similarity=0.310 Sum_probs=31.7
Q ss_pred EEEEEEeCCCccceeech------------HHHHHHHHcCCCcceeeecCC
Q psy10165 219 TKIFVEKKPEGTGLICHR------------IIQEICKAVGIKDIRAKVEGS 257 (337)
Q Consensus 219 tkV~l~PaP~G~Glva~~------------~ir~Il~laGIkDv~aKv~Gs 257 (337)
+.+++.|...|.||...- ..+.-|-.|||+|+..++-.-
T Consensus 53 SSa~V~~~~~g~Gi~V~i~tp~NIt~VT~~mY~NAl~TAGv~da~I~Vasp 103 (225)
T PF06207_consen 53 SSAYVTPTDKGSGIKVEIVTPNNITWVTEEMYANALITAGVTDADIYVASP 103 (225)
T ss_pred EEEEEEECCCCCCeEEEEeccCcceeecHHHHHHHHHHcCCCcceEEEecc
Confidence 457788999999987755 677889999999999887653
No 20
>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=26.58 E-value=1.6e+02 Score=24.51 Aligned_cols=42 Identities=21% Similarity=0.276 Sum_probs=28.0
Q ss_pred EEceEEEEEEeCCCccceeechHHHHHHHHcCCCcceeeecCCCChhhHHHHHHHHHh
Q psy10165 215 QFGKTKIFVEKKPEGTGLICHRIIQEICKAVGIKDIRAKVEGSTNPQAIVKAFFLGLM 272 (337)
Q Consensus 215 k~gstkV~l~PaP~G~Glva~~~ir~Il~laGIkDv~aKv~Gstn~~NvvkAtf~AL~ 272 (337)
+|+.+.+.|.|.++|.|+. +..++.|-.-|-+++.|+-+++.
T Consensus 24 ~~a~v~l~veP~~~g~g~~----------------f~~~~~~~~ip~~~~~aie~g~~ 65 (115)
T cd01684 24 FWATVGLRVEPLPRGSGLQ----------------YESEVSLGSLPRSFQNAVEETVR 65 (115)
T ss_pred EEEEEEEEEEECCCCCCcE----------------EEEEecCCcCCHHHHHHHHHHHH
Confidence 3999999999999885443 22344454456666766666654
No 21
>KOG4328|consensus
Probab=26.46 E-value=1e+02 Score=32.54 Aligned_cols=35 Identities=20% Similarity=0.243 Sum_probs=26.2
Q ss_pred EEEEEeeeeeeecCCCceEEEE-------EEEEEeCCCCceeee
Q psy10165 139 RILEYKAVFCMKKNSGRYRTVS-------TLVVTGNGQGLAGFA 175 (337)
Q Consensus 139 ~VL~v~rV~kmT~~~GR~~rf~-------alVvVGNgnG~vG~G 175 (337)
-.+..-.|.++|. ||+++.. -+|++||+.|.|||-
T Consensus 174 ~~~~~~~v~kv~~--~Rit~l~fHPt~~~~lva~GdK~G~VG~W 215 (498)
T KOG4328|consen 174 DDYRILNVAKVTD--RRITSLAFHPTENRKLVAVGDKGGQVGLW 215 (498)
T ss_pred ccceecceeEecc--cceEEEEecccCcceEEEEccCCCcEEEE
Confidence 3444455677775 8888763 799999999999984
No 22
>PRK13832 plasmid partitioning protein; Provisional
Probab=24.57 E-value=2.7e+02 Score=29.85 Aligned_cols=71 Identities=15% Similarity=0.134 Sum_probs=49.0
Q ss_pred EEeCCCc---cceeechHHHHHHHHcCCCcceeeecCCC------------------ChhhHHHHHHHHHhcCCCHHHHH
Q psy10165 223 VEKKPEG---TGLICHRIIQEICKAVGIKDIRAKVEGST------------------NPQAIVKAFFLGLMQQKSHQQLA 281 (337)
Q Consensus 223 l~PaP~G---~Glva~~~ir~Il~laGIkDv~aKv~Gst------------------n~~NvvkAtf~AL~~~~t~~~iA 281 (337)
++|.+.| |.|+|+..=...+.++|...+-+.+.-.. ||.--+.|+-.-+..-.|.++||
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 3454443 78999887666788999998887775332 22223344444445678999999
Q ss_pred HHhCCchhhhcc
Q psy10165 282 EEQQLHLVEFSE 293 (337)
Q Consensus 282 ~~rG~~vve~~~ 293 (337)
...|++...++.
T Consensus 126 ~~lG~S~~~V~r 137 (520)
T PRK13832 126 VALALPVRQIRK 137 (520)
T ss_pred HHHCCCHHHHHH
Confidence 999999877764
No 23
>PF06754 PhnG: Phosphonate metabolism protein PhnG; InterPro: IPR009609 This family consists of several bacterial phosphonate metabolism protein PhnG sequences. In Escherichia coli, the phn operon encodes proteins responsible for the uptake and breakdown of phosphonates. The exact function of PhnG is unknown, however it is thought likely that along with six other proteins PhnG makes up the the C-P (carbon-phosphorus) lyase [].; GO: 0015716 phosphonate transport, 0019634 phosphonate metabolic process
Probab=24.37 E-value=1.7e+02 Score=25.98 Aligned_cols=42 Identities=17% Similarity=0.093 Sum_probs=36.1
Q ss_pred CCceEEEEEEEEEeCCCCceeeecccchhHHHHHHHHHHHHccC
Q psy10165 153 SGRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQK 196 (337)
Q Consensus 153 ~GR~~rf~alVvVGNgnG~vG~G~GKa~ev~~AirkA~~~Ak~n 196 (337)
.|-..=-+|.|-+.| |.+|+|+-.+.+..-|.--|+.+|...
T Consensus 59 LGEv~VTr~~V~l~~--g~~G~~~v~G~d~~~A~~~Av~DAllq 100 (146)
T PF06754_consen 59 LGEVTVTRCAVRLED--GTVGYGYVLGRDKRHAELAAVIDALLQ 100 (146)
T ss_pred cceEEEEEEEEEeCC--CCEEEEEEcCCCHHHHHHHHHHHHHhC
Confidence 577777788888888 779999999999999999999999753
No 24
>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=22.97 E-value=1.1e+02 Score=29.26 Aligned_cols=35 Identities=11% Similarity=0.174 Sum_probs=30.1
Q ss_pred CCCCceeeecccchhHHHHHHHHHHHHccCcEEEe
Q psy10165 167 NGQGLAGFALGKSVEGRASMRNAKNRAGQKLIYVQ 201 (337)
Q Consensus 167 NgnG~vG~G~GKa~ev~~AirkA~~~Ak~nli~V~ 201 (337)
+..+..-+|.|++.+...|+.+|+..|.+......
T Consensus 198 ~~~~~~~~G~ga~~~~~~Al~rAl~E~~q~~~~~~ 232 (332)
T PF02624_consen 198 KDRPYYAVGAGAHLDPEEALERALTEAAQSRLLFI 232 (332)
T ss_pred CCCcceEEEeccCCCHHHHHHHHHHHHHHHHHHHH
Confidence 57777999999999999999999999987666555
No 25
>TIGR00607 rad52 recombination protein rad52. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.64 E-value=2.9e+02 Score=25.25 Aligned_cols=73 Identities=16% Similarity=0.280 Sum_probs=37.0
Q ss_pred ccccCccccccc----ccCCCcceEEEEEeeeeeeecCCCceEE--EEEEE--EEeCCCCc--eeeeccc-chhHHHHHH
Q psy10165 119 ARDLNRGQIIGI----DTFDGFDTRILEYKAVFCMKKNSGRYRT--VSTLV--VTGNGQGL--AGFALGK-SVEGRASMR 187 (337)
Q Consensus 119 ~~~l~~~eiId~----~~~~~f~~~VL~v~rV~kmT~~~GR~~r--f~alV--vVGNgnG~--vG~G~GK-a~ev~~Air 187 (337)
..+|.....|.+ |-|+++...|+++..-+--.. .| +++ ++|+| ..=||.=+ +|+|... .+.-..|+.
T Consensus 26 v~Yieg~k~i~lANeiFGFnGWSs~I~~~~vd~~de~-~~-k~~vg~saiVRVtLkDGt~~EdiG~G~~~n~~~K~~A~e 103 (161)
T TIGR00607 26 VCYIEGWKVINLANEIFGYNGWSHSITQQNVDFVDEN-NG-KFSVGVCAIVRVTLKDGSYHEDVGYGVSENLRSKALAFE 103 (161)
T ss_pred EEeccHHHHHHHHHHhcCCCCceeeeeecccceeccc-CC-cEEEEEEEEEEEEEcCCcEeecccceeeecCCcHHHHHH
Confidence 356666666653 778999999998854222222 33 222 22222 22344333 4555444 223345555
Q ss_pred HHHHHH
Q psy10165 188 NAKNRA 193 (337)
Q Consensus 188 kA~~~A 193 (337)
+|+..|
T Consensus 104 kAKKeA 109 (161)
T TIGR00607 104 KAKKEA 109 (161)
T ss_pred HHHHHH
Confidence 555544
No 26
>COG0350 Ada Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=20.77 E-value=1.5e+02 Score=26.74 Aligned_cols=69 Identities=13% Similarity=0.118 Sum_probs=47.4
Q ss_pred hhHHHHHHHHHhc-----CCCHHHHHHHhCCch----hhhccccCCcceeeecCCCcCCCCCCC-CCh-hhhhccccchh
Q psy10165 261 QAIVKAFFLGLMQ-----QKSHQQLAEEQQLHL----VEFSEENDNYPTIVASPSTCKKDSSKA-PDF-TEVSSWSYRPE 329 (337)
Q Consensus 261 ~NvvkAtf~AL~~-----~~t~~~iA~~rG~~v----ve~~~e~~~~p~vvasp~~~~~~~~~~-~~~-~~~~~~~~~~~ 329 (337)
..+.+.+.++|.+ ..||.|||+.-|..- |=-.-..+++|+||--=..+.++.+.. ..| -+.|+|+.+.|
T Consensus 87 t~Fq~~Vw~aL~~IP~Get~TY~eiA~~ig~p~a~rAVG~A~~~NPl~IiIPCHRVig~~G~L~Gy~~G~~~K~~LL~~E 166 (168)
T COG0350 87 TGFQGRVWQALREIPYGETVTYGEIARRLGRPTAVRAVGNANGANPLPIIIPCHRVIGADGDLGGYAGGLERKKWLLELE 166 (168)
T ss_pred ChHHHHHHHHHhcCCCCCcEeHHHHHHHhCCCcHHHHHHHHhccCCceEEecCeEeEcCCCCccCccchHHHHHHHHHhh
Confidence 3677888888886 579999999999822 333345667777775546677776653 555 66777776554
No 27
>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=20.57 E-value=5.2e+02 Score=23.72 Aligned_cols=132 Identities=13% Similarity=0.152 Sum_probs=71.6
Q ss_pred CCceEEEEEEEEEeCCCCceeeecccchhHHHHHHHHHHHHccCcEEEeccCCcceeEeEEEEEceEEEEEEeCCCccce
Q psy10165 153 SGRYRTVSTLVVTGNGQGLAGFALGKSVEGRASMRNAKNRAGQKLIYVQRYKDHTVLHDFYTQFGKTKIFVEKKPEGTGL 232 (337)
Q Consensus 153 ~GR~~rf~alVvVGNgnG~vG~G~GKa~ev~~AirkA~~~Ak~nli~V~r~~~~TIph~v~gk~gstkV~l~PaP~G~Gl 232 (337)
.-.-.+.+++|+.+|.-|- +.+.+.++..|++.. +.+.+.++..--.. .+ -...--+.+-+|.+.|... .|+
T Consensus 41 a~~d~~ik~vvL~~~s~gg---~~~~~~el~~~i~~~-~~~~kpVia~~~~~-~s--ggy~lasaad~I~a~p~~~-vg~ 112 (222)
T cd07018 41 AAEDDRIKGIVLDLDGLSG---GLAKLEELRQALERF-RASGKPVIAYADGY-SQ--GQYYLASAADEIYLNPSGS-VEL 112 (222)
T ss_pred HhcCCCeEEEEEECCCCCC---CHHHHHHHHHHHHHH-HHhCCeEEEEeCCC-Cc--hhhhhhhhCCEEEECCCce-EEe
Confidence 3445578999999987543 777778888888764 33555554432111 01 1111122344666655322 444
Q ss_pred e----echHHHHHHHHcCCCcceeeecCCC---Chh------hHHHHHHHHHhc-C--CCHHHHHHHhCCchhhhc
Q psy10165 233 I----CHRIIQEICKAVGIKDIRAKVEGST---NPQ------AIVKAFFLGLMQ-Q--KSHQQLAEEQQLHLVEFS 292 (337)
Q Consensus 233 v----a~~~ir~Il~laGIkDv~aKv~Gst---n~~------NvvkAtf~AL~~-~--~t~~~iA~~rG~~vve~~ 292 (337)
+ -+.-++.+++.+||+-=..++--.. +|+ --.+..++++.. . .-.+.+|+.|++...++.
T Consensus 113 iGv~~~~~~~~~ll~klGv~~~~~~~G~~K~~~~~~~~~~~s~~~r~~~~~~l~~~~~~f~~~Va~~R~~~~~~~~ 188 (222)
T cd07018 113 TGLSAETLFFKGLLDKLGVEVQVFRVGEYKSAVEPFTRDDMSPEAREQTQALLDSLWDQYLADVAASRGLSPDALE 188 (222)
T ss_pred eccchhhhhHHHHHHHcCCcEEEEEEeccccccchhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHH
Confidence 3 2557899999999996444332111 222 112333333332 1 225678888887766554
Done!