Query 013474
Match_columns 442
No_of_seqs 189 out of 657
Neff 2.4
Searched_HMMs 46136
Date Fri Mar 29 04:13:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013474.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013474hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2646 Ribosomal protein S5 [ 100.0 5.2E-40 1.1E-44 324.9 -3.2 353 3-431 1-362 (396)
2 PTZ00070 40S ribosomal protein 100.0 1.7E-32 3.7E-37 261.4 6.2 101 326-442 33-134 (257)
3 TIGR01020 rpsE_arch ribosomal 100.0 5.8E-32 1.3E-36 252.0 6.7 100 326-442 4-104 (212)
4 PRK04044 rps5p 30S ribosomal p 100.0 1.7E-30 3.7E-35 241.9 7.0 99 327-442 6-104 (211)
5 KOG0877 40S ribosomal protein 99.9 9.7E-26 2.1E-30 210.3 2.9 101 325-441 4-104 (213)
6 COG0098 RpsE Ribosomal protein 99.8 1.7E-21 3.6E-26 179.0 5.4 77 344-442 2-78 (181)
7 PF00333 Ribosomal_S5: Ribosom 99.8 1E-19 2.3E-24 143.5 5.3 56 387-442 1-56 (67)
8 CHL00138 rps5 ribosomal protei 99.7 2E-18 4.4E-23 153.2 6.0 58 385-442 21-78 (143)
9 TIGR01021 rpsE_bact ribosomal 99.7 1.9E-18 4.2E-23 154.3 5.9 56 387-442 1-56 (154)
10 PRK00550 rpsE 30S ribosomal pr 99.7 5.8E-18 1.2E-22 153.2 6.0 58 385-442 10-67 (168)
11 KOG2646 Ribosomal protein S5 [ 98.6 1.1E-08 2.5E-13 103.3 1.3 57 386-442 180-239 (396)
12 KOG0772 Uncharacterized conser 70.1 1.7 3.7E-05 47.4 0.6 18 132-151 99-116 (641)
13 PF02624 YcaO: YcaO-like famil 64.0 22 0.00048 33.7 6.6 105 301-441 116-221 (332)
14 PF08031 BBE: Berberine and be 60.0 3.7 7.9E-05 30.4 0.5 15 265-279 24-38 (47)
15 PF04979 IPP-2: Protein phosph 53.9 9.1 0.0002 32.5 2.0 57 140-201 50-106 (132)
16 KOG0341 DEAD-box protein abstr 45.8 41 0.0009 36.6 5.6 92 112-213 3-115 (610)
17 PF11802 CENP-K: Centromere-as 38.4 29 0.00062 35.1 3.0 39 218-257 172-231 (268)
18 cd00048 DSRM Double-stranded R 38.3 39 0.00085 24.1 3.0 28 404-433 28-55 (68)
19 smart00358 DSRM Double-strande 36.7 31 0.00067 24.9 2.3 28 405-434 27-54 (67)
20 PF05553 DUF761: Cotton fibre 34.2 52 0.0011 24.5 3.1 21 183-203 2-22 (38)
21 KOG1945 Protein phosphatase 1 33.9 28 0.00061 36.7 2.2 61 28-96 24-90 (377)
22 TIGR03604 docking_ocin bacteri 32.1 1.3E+02 0.0028 30.3 6.5 105 300-441 117-222 (377)
23 PF03656 Pam16: Pam16; InterP 29.1 1.3E+02 0.0028 27.2 5.3 49 210-270 54-108 (127)
24 PF07710 P53_tetramer: P53 tet 27.4 45 0.00098 25.4 1.8 22 251-272 16-37 (42)
25 TIGR00702 uncharacterized doma 23.7 1.3E+02 0.0029 30.6 4.9 104 300-441 159-262 (377)
26 PF15463 ECM11: Extracellular 21.8 3.5E+02 0.0075 24.1 6.6 56 315-374 59-119 (139)
27 KOG3228 Uncharacterized conser 21.4 8.4E+02 0.018 24.5 10.8 25 91-115 41-65 (226)
28 COG3655 Predicted transcriptio 20.7 76 0.0016 26.6 2.1 38 242-281 30-71 (73)
29 PF14131 DUF4298: Domain of un 20.4 1.3E+02 0.0028 25.2 3.4 21 189-209 1-21 (90)
30 PF04931 DNA_pol_phi: DNA poly 20.3 2.1E+02 0.0046 31.9 6.0 12 103-114 622-633 (784)
31 PF04450 BSP: Peptidase of pla 20.3 95 0.0021 29.7 2.9 94 173-271 70-184 (205)
No 1
>KOG2646 consensus Ribosomal protein S5 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.2e-40 Score=324.95 Aligned_cols=353 Identities=35% Similarity=0.410 Sum_probs=305.7
Q ss_pred CCCCcchhhHHHHhhccCCCCCCCCccc-ccccCCCC-------ccCCCCCCCCCCCCCCCCCccccccccccccccccc
Q 013474 3 NKTRPFSWSRLLLNQNLKNPTKTPLSFS-RKISTFPH-------FLTNQTPPNPLPPRTHFPNASQEYSAKPIYSFSRKI 74 (442)
Q Consensus 3 ~~~~~~~~~r~l~~~~~~~~~~~~~~~~-~~~~~~~~-------f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 74 (442)
.+|+..+|.|+++++++.+.+...+..+ ..++|+|. ||.||||| .+ ||
T Consensus 1 ~~t~~s~~~r~~~Rr~~~s~~s~~lnt~~ss~~t~~~~~~ses~~~~~~t~~-------~~---sQ-------------- 56 (396)
T KOG2646|consen 1 LRTRASSWPRLLSRRNPTSSFSRLLNTLDSSLKTRPRGYYSESLFPVNQTPW-------IS---SQ-------------- 56 (396)
T ss_pred CccchhhHHHHHhhcCCchhhhHHhhhcccccccccccccchhhccccCchh-------hh---cC--------------
Confidence 3689999999999999998877777777 67778755 88888877 22 11
Q ss_pred cccccccccCCCCcccccccccccCccchHHHHHHHHHHHHHHhHHHHHHHHcCCCCcCCCcccccccccchhHHHHHHH
Q 013474 75 STFSHFRYNQTSKPSILLKSHFSTGSAYSRVAQDLLAEVEREKGREREARKRQGLDTKDIDQEDEEDYMGVGPLIEKLEK 154 (442)
Q Consensus 75 ~~~~~~~~~~~~~~~~~~~~~fs~~~~~~~v~~~ll~evere~~rer~~r~r~g~d~~d~d~e~eedy~gv~plieklek 154 (442)
++|-.++|+-+ ++++ +|++|++.+++++.+.|.+.+++.++|++++|++| ..|+|.+
T Consensus 57 -------------~~rP~st~~r~--~ad~---~l~a~~~~ek~~k~~~r~~e~~~~~~i~aq~ede~--~e~fi~~--- 113 (396)
T KOG2646|consen 57 -------------QYRPFSTFSRS--EADR---ELIAEVAKEKQRKIEERQREKLDYKDIDAQDEDEY--REPFIWK--- 113 (396)
T ss_pred -------------ccccccccccc--cCCh---hhccchhhhhccccchhhhhcCCchhhhhhhhhhh--hhhcccC---
Confidence 11112222222 2333 89999999999999999999999999999999999 9999988
Q ss_pred hhhcccCCCCCccCCCCCCCchhhcccChHHHHHhHHHHHHHHHhHHHHHHhhhhcCChhHHHHHhhhhhhhhhccCCCC
Q 013474 155 ERLKDTGDLNLYEEPTDSDSDEDDERFSRDAVNKRFQVFQKKFKRHKELLQNFTEAETPDEAFKWMNKIDKFEQKHFPLR 234 (442)
Q Consensus 155 ~~~k~~~~~~~~~e~tdsdsd~d~e~~~~d~~~kr~~~f~~k~~rh~ell~~f~~aetld~a~k~m~kid~fe~kh~~l~ 234 (442)
..|++.|.+++..+..|+++..++. +.|.-.+..|.|.++++.|..+.+.-+.++++|+|+.||+.+|. |.+||+|
T Consensus 114 ~pL~~~g~~k~~~ers~~~ke~~~~--dld~~r~~~D~~~k~~~G~~~~k~~~~k~g~~~e~~~~~n~~Df-e~r~l~l- 189 (396)
T KOG2646|consen 114 QPLKDDGELKRIAERSDSGKENDEI--DLDEERKKEDIFSKKERGHSGLKWTDTKLGLPDEAFRGMNYLDF-ELRHLEL- 189 (396)
T ss_pred CccchhhhhhhhhcccCcccccccc--hhhhhhhhhhccCchhcCCCcccccccccCCCCccccCCCchhh-hHHHHHH-
Confidence 9999999999999999999998888 89999999999999999999999999999999999999999995 9999999
Q ss_pred chhhHHHHHHHHhHhhhccchhHHHHHHHhHhhhhhhhhccCCCCCCCccceeeccCCCChhhhhhhhhhHHH-hhhcCC
Q 013474 235 HEYRVIGELMNRLKEAEGKDKFMLQQKLNRAMRLVEWKEVYDPNNPTNYGVIRHEQAGPNVDAVENAEMDEEK-RLLQGG 313 (442)
Q Consensus 235 ~eyrvig~lmnrlk~aegkd~f~l~~klnra~rl~e~keaydp~npanyg~i~~~q~g~~~d~~~~a~~~~ek-~~~~g~ 313 (442)
||++++||||++.+.++..||+++++|+||+|+|||++ ||++||+|++|-++. ..-.+.+++. +-|-|.
T Consensus 190 --vrr~~~~~~r~Gki~s~~~LVvvGn~nGaaG~~eGKa~-~~~s~A~~ka~~rAv-------~~l~~ieRyE~rTiygD 259 (396)
T KOG2646|consen 190 --VRRRVENQNRKGKIASMYALVVVGNGNGAAGLGEGKAA-DPNSPAIYKAIGRAV-------RNLGYIERYERRTIYGD 259 (396)
T ss_pred --HHhhhhccccccceeeEEEEEEEecCCcceeeccccCc-CccCHHHHHHHHHHH-------hhcCccccccCcccccc
Confidence 99999999999999999999999999999999999999 999999999987654 4445566654 458887
Q ss_pred CCCCChHHhhhhhhhhhHHHHHHHhHhHhhhhhhhhhHHhhccCCccchHHHHHHHHHhhhhhhhcccccccCCcceeee
Q 013474 314 VDDDDEEEFDDMKERDDILLERLNAIDKKLEEKLAELDHTFGKKGKLLEEEIRDLAEERNALTEKKRRPLYRKGFDVKLI 393 (442)
Q Consensus 314 ~d~~~eeEf~d~kEkd~i~itKLg~ivKk~EGKI~sLdeiF~k~~pIlE~EIVD~LeerN~Ltekkr~p~~lp~LkEeVL 393 (442)
-|++..+++.+|+++......++|.+..++...+--.|..+...+.+.+-+|+..+.++|.+++.+..+.+..++ .||
T Consensus 260 i~~r~~~~~l~mk~rp~GfGLrcn~il~kIC~~~GIKDis~kv~GsrN~m~i~k~~~e~l~~qet~qqlA~rkG~--hvV 337 (396)
T KOG2646|consen 260 IDDRFHEVRLDMKSRPDGFGLRCNPILIKICECAGIKDISGKVKGSRNEMNITKAAFEALALQETHQQLAYRKGL--HVV 337 (396)
T ss_pred chhhhhhhhhhhhhCCCcccccccHHHHHHHHHhccccccceeeccchHHHHHHHHHHHHhhhhhhHHHHHhcCC--eEE
Confidence 799999999999999999999999999999999999999999999999999999999999999988887555433 788
Q ss_pred EeecceeeccCCeeEEEEEEEEEecCCCceeeeeccCC
Q 013474 394 DVNRTCKVTKGGQVVKYTAMLACGNYHGVVGFAKAKGP 431 (442)
Q Consensus 394 dInRVQKmTKgGRRtRFrALVVVGNgNG~VGlGvGKAK 431 (442)
+|. |++.+.. ||.-|.+|+...++.
T Consensus 338 dVr--------~e~~~~t-----~~vaspig~~~k~~e 362 (396)
T KOG2646|consen 338 DVR--------GEVYRLT-----GNVASPIGYAKKKAE 362 (396)
T ss_pred Eec--------cceeecc-----cceecccchhhcCCc
Confidence 887 3333332 888999999988764
No 2
>PTZ00070 40S ribosomal protein S2; Provisional
Probab=99.97 E-value=1.7e-32 Score=261.39 Aligned_cols=101 Identities=19% Similarity=0.295 Sum_probs=96.0
Q ss_pred hhhhhHHHHHHHhHhHhhhhhhhhhHHhhccCCccchHHHHHHHHHhhhhhhhccccccc-CCcceeeeEeecceeeccC
Q 013474 326 KERDDILLERLNAIDKKLEEKLAELDHTFGKKGKLLEEEIRDLAEERNALTEKKRRPLYR-KGFDVKLIDVNRTCKVTKG 404 (442)
Q Consensus 326 kEkd~i~itKLg~ivKk~EGKI~sLdeiF~k~~pIlE~EIVD~LeerN~Ltekkr~p~~l-p~LkEeVLdInRVQKmTKg 404 (442)
++++|+|+||||+||| +|||+|||++|..++||+|+||||+| +. ++|+++||+|++|||||++
T Consensus 33 ~~~~W~P~TklGrlVk--~gki~s~eei~~~~lpikE~eIvd~l--------------l~~~~L~eeVl~I~rVqK~Tkg 96 (257)
T PTZ00070 33 EEKEWVPVTKLGRLVK--AGKITSLEEIFLFSIPIKEYQIVDHF--------------FAESKLKDEVMKIMPVQKQTSA 96 (257)
T ss_pred ccCceeeccchhhhhh--cCccccHHHHHhcCCCccchhhHHHH--------------ccCccchheEEEEeeeEEEecC
Confidence 4578999999999999 55999999999999999999999999 22 7999999999999999999
Q ss_pred CeeEEEEEEEEEecCCCceeeeeccCCcHHHHhhhhcC
Q 013474 405 GQVVKYTAMLACGNYHGVVGFAKAKGPAVPIALQKVTW 442 (442)
Q Consensus 405 GRRtRFrALVVVGNgNG~VGlGvGKAKEVatAIrKAIW 442 (442)
||++||+|||||||+||+||||+|||+||++||+||++
T Consensus 97 Grr~rF~AlVVVGd~nG~VGlG~gKakEV~~AIrKAi~ 134 (257)
T PTZ00070 97 GQRTRFKAFVVVGDGNGHIGLGAKVAKEVATAIRGAII 134 (257)
T ss_pred CcEEEEEEEEEEeCCCCcEecceeechhHHHHHHHHHH
Confidence 99999999999999999999999999999999999984
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=99.97 E-value=5.8e-32 Score=251.99 Aligned_cols=100 Identities=24% Similarity=0.365 Sum_probs=95.1
Q ss_pred hhhhhHHHHHHHhHhHhhhhhhhhhHHhhccCCccchHHHHHHHHHhhhhhhhcccccccCCc-ceeeeEeecceeeccC
Q 013474 326 KERDDILLERLNAIDKKLEEKLAELDHTFGKKGKLLEEEIRDLAEERNALTEKKRRPLYRKGF-DVKLIDVNRTCKVTKG 404 (442)
Q Consensus 326 kEkd~i~itKLg~ivKk~EGKI~sLdeiF~k~~pIlE~EIVD~LeerN~Ltekkr~p~~lp~L-kEeVLdInRVQKmTKg 404 (442)
++++|.|.||||+||| +|||+|||++|..++||+|+||||+| +++| +++||+|+||||||++
T Consensus 4 ~~~~w~p~t~lgrlV~--~g~i~s~~ei~~~~~~i~E~eivd~l---------------l~~l~~e~vl~I~rV~K~tkg 66 (212)
T TIGR01020 4 ELEEWVPRTKLGRLVK--EGKIKSIDEIFLRNLPIKEPEIVDYL---------------LPDLNEEEVLDVSLVQRMTDS 66 (212)
T ss_pred cccCeeecchhhhhhh--cCCcccHHHHHHcCCCccchhhHHHH---------------hhhcCcceEEEEEeeEEEecC
Confidence 3456999999999999 56999999999999999999999999 7899 7799999999999999
Q ss_pred CeeEEEEEEEEEecCCCceeeeeccCCcHHHHhhhhcC
Q 013474 405 GQVVKYTAMLACGNYHGVVGFAKAKGPAVPIALQKVTW 442 (442)
Q Consensus 405 GRRtRFrALVVVGNgNG~VGlGvGKAKEVatAIrKAIW 442 (442)
||++||+|||||||+||+||||+|||+||+.||+||++
T Consensus 67 Gr~~~F~alVvVGn~~G~vG~G~GKa~ev~~AI~kA~~ 104 (212)
T TIGR01020 67 GRRTRFRAFVVVGNRDGYVGLGIGKAKEVAPAIRKAII 104 (212)
T ss_pred CcEEEEEEEEEEeCCCCeEeeceeecchHHHHHHHHHH
Confidence 99999999999999999999999999999999999974
No 4
>PRK04044 rps5p 30S ribosomal protein S5P; Reviewed
Probab=99.96 E-value=1.7e-30 Score=241.93 Aligned_cols=99 Identities=25% Similarity=0.372 Sum_probs=95.1
Q ss_pred hhhhHHHHHHHhHhHhhhhhhhhhHHhhccCCccchHHHHHHHHHhhhhhhhcccccccCCcceeeeEeecceeeccCCe
Q 013474 327 ERDDILLERLNAIDKKLEEKLAELDHTFGKKGKLLEEEIRDLAEERNALTEKKRRPLYRKGFDVKLIDVNRTCKVTKGGQ 406 (442)
Q Consensus 327 Ekd~i~itKLg~ivKk~EGKI~sLdeiF~k~~pIlE~EIVD~LeerN~Ltekkr~p~~lp~LkEeVLdInRVQKmTKgGR 406 (442)
+++|.|.||||++|| +|+|+|||++|.++.||.|+||||.| +++|+++||+|+||||||++||
T Consensus 6 ~~~w~p~t~lg~lv~--~~~i~s~e~i~~~~~~i~e~eivd~l---------------l~~l~e~vv~i~rV~kvtkgGr 68 (211)
T PRK04044 6 IEEWEPKTRLGRLVK--EGKITSIDEIFDSGLPIKEPEIVDVL---------------LPDLEDEVLDINMVQRMTDSGR 68 (211)
T ss_pred ccCccccchhhhhhh--cCCcccHHHHHhcCCCcccchhhhhh---------------hccceeEEEEEEeEEeeecCCc
Confidence 456999999999999 55999999999999999999999999 7899999999999999999999
Q ss_pred eEEEEEEEEEecCCCceeeeeccCCcHHHHhhhhcC
Q 013474 407 VVKYTAMLACGNYHGVVGFAKAKGPAVPIALQKVTW 442 (442)
Q Consensus 407 RtRFrALVVVGNgNG~VGlGvGKAKEVatAIrKAIW 442 (442)
+++|+|||||||+||+||||+|||+||++||+||++
T Consensus 69 ~~sf~alVvVGn~~G~vG~G~GKa~ev~~Ai~kA~~ 104 (211)
T PRK04044 69 RVRFRVVVVVGNRDGYVGVGQGKAKQVGPAIRKAIR 104 (211)
T ss_pred EEEEEEEEEEeCCCCeEeeeeeeccchHHHHHHHHH
Confidence 999999999999999999999999999999999974
No 5
>KOG0877 consensus 40S ribosomal protein S2/30S ribosomal protein S5 [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=9.7e-26 Score=210.32 Aligned_cols=101 Identities=22% Similarity=0.353 Sum_probs=96.2
Q ss_pred hhhhhhHHHHHHHhHhHhhhhhhhhhHHhhccCCccchHHHHHHHHHhhhhhhhcccccccCCcceeeeEeecceeeccC
Q 013474 325 MKERDDILLERLNAIDKKLEEKLAELDHTFGKKGKLLEEEIRDLAEERNALTEKKRRPLYRKGFDVKLIDVNRTCKVTKG 404 (442)
Q Consensus 325 ~kEkd~i~itKLg~ivKk~EGKI~sLdeiF~k~~pIlE~EIVD~LeerN~Ltekkr~p~~lp~LkEeVLdInRVQKmTKg 404 (442)
.++..|.|.+|||+++|.+ ||+++++++..++||.|+||+|++ ..+.|+++||+|++|||||++
T Consensus 4 ~~~~~~~p~t~lG~lv~~~--ki~sleeiyl~slpike~eiid~~--------------lg~slkdeVLkImpVqKqtrA 67 (213)
T KOG0877|consen 4 PEEKEWMPVTKLGRLVKDM--KIKSLEEIYLFSLPIKESEIIDFF--------------LGASLKDEVLKIMPVQKQTRA 67 (213)
T ss_pred CccCcCCCcccccccchhc--hhhhhhhhhccCccccchhhhhhh--------------hccchHhhhheeeeccccccc
Confidence 4678999999999999966 888999999999999999999999 457899999999999999999
Q ss_pred CeeEEEEEEEEEecCCCceeeeeccCCcHHHHhhhhc
Q 013474 405 GQVVKYTAMLACGNYHGVVGFAKAKGPAVPIALQKVT 441 (442)
Q Consensus 405 GRRtRFrALVVVGNgNG~VGlGvGKAKEVatAIrKAI 441 (442)
|+++||+|+|+|||+|||||+|+.|++||++||++||
T Consensus 68 GQrtRfKAfVaigD~~ghVGlgvk~sKeva~airgai 104 (213)
T KOG0877|consen 68 GQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAI 104 (213)
T ss_pred ccccceEEEEEEeecCCceeeeeeehHHHHHHHhHHH
Confidence 9999999999999999999999999999999999986
No 6
>COG0098 RpsE Ribosomal protein S5 [Translation, ribosomal structure and biogenesis]
Probab=99.84 E-value=1.7e-21 Score=178.96 Aligned_cols=77 Identities=35% Similarity=0.544 Sum_probs=70.9
Q ss_pred hhhhhhhHHhhccCCccchHHHHHHHHHhhhhhhhcccccccCCcceeeeEeecceeeccCCeeEEEEEEEEEecCCCce
Q 013474 344 EEKLAELDHTFGKKGKLLEEEIRDLAEERNALTEKKRRPLYRKGFDVKLIDVNRTCKVTKGGQVVKYTAMLACGNYHGVV 423 (442)
Q Consensus 344 EGKI~sLdeiF~k~~pIlE~EIVD~LeerN~Ltekkr~p~~lp~LkEeVLdInRVQKmTKgGRRtRFrALVVVGNgNG~V 423 (442)
++++++++ |..++++.|++ +|.| .++||+|+||||||++||++||+|||||||+||+|
T Consensus 2 ~~~~~~~~--~~~~~~~~e~~-~~~l-------------------~e~vv~inrV~K~~kgGRr~~F~alvVVGd~~G~V 59 (181)
T COG0098 2 EGKIATIE--FKSGLPIKEPE-VDEL-------------------LEKVVDINRVSKVVKGGRRFRFSALVVVGDRNGRV 59 (181)
T ss_pred Cccccchh--hhhccCcCCch-hhhc-------------------ceeeeEEEEEEEeecCceEEEEEEEEEEeCCCCeE
Confidence 56788888 99999999999 5555 34799999999999999999999999999999999
Q ss_pred eeeeccCCcHHHHhhhhcC
Q 013474 424 GFAKAKGPAVPIALQKVTW 442 (442)
Q Consensus 424 GlGvGKAKEVatAIrKAIW 442 (442)
|||+|||+||+.||+||+|
T Consensus 60 G~G~GKA~EV~~AIrKAi~ 78 (181)
T COG0098 60 GFGIGKAKEVPEAIRKAIE 78 (181)
T ss_pred eeeecchhhhHHHHHHHHH
Confidence 9999999999999999986
No 7
>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=99.79 E-value=1e-19 Score=143.53 Aligned_cols=56 Identities=36% Similarity=0.679 Sum_probs=54.1
Q ss_pred CcceeeeEeecceeeccCCeeEEEEEEEEEecCCCceeeeeccCCcHHHHhhhhcC
Q 013474 387 GFDVKLIDVNRTCKVTKGGQVVKYTAMLACGNYHGVVGFAKAKGPAVPIALQKVTW 442 (442)
Q Consensus 387 ~LkEeVLdInRVQKmTKgGRRtRFrALVVVGNgNG~VGlGvGKAKEVatAIrKAIW 442 (442)
+|+++||+|+|||+||++||+++|+|||||||+||+||||+|||.+++.||+||++
T Consensus 1 ~l~~~vl~v~rv~k~tk~Gr~~~~~alvvvGn~~G~vG~G~gKa~~~~~Ai~kA~~ 56 (67)
T PF00333_consen 1 DLEEKVLEVKRVSKMTKGGRIFSFRALVVVGNGNGLVGFGVGKAKEVPDAIRKAKR 56 (67)
T ss_dssp SHEEEEEEEEEEEEEETTEEEEEEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHH
T ss_pred CceEEEEEEEEEEEEecCCceeEEEEEEEEecCCCcEecCcccchhHHHHHHHHHH
Confidence 58899999999999999999999999999999999999999999999999999964
No 8
>CHL00138 rps5 ribosomal protein S5; Validated
Probab=99.74 E-value=2e-18 Score=153.17 Aligned_cols=58 Identities=29% Similarity=0.511 Sum_probs=56.3
Q ss_pred cCCcceeeeEeecceeeccCCeeEEEEEEEEEecCCCceeeeeccCCcHHHHhhhhcC
Q 013474 385 RKGFDVKLIDVNRTCKVTKGGQVVKYTAMLACGNYHGVVGFAKAKGPAVPIALQKVTW 442 (442)
Q Consensus 385 lp~LkEeVLdInRVQKmTKgGRRtRFrALVVVGNgNG~VGlGvGKAKEVatAIrKAIW 442 (442)
.++|+++||+|+||||||++||+++|+|||||||+||+||||+|||.|+++||+||++
T Consensus 21 ~~~l~ekvl~i~rV~k~tkgGR~~~f~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~ 78 (143)
T CHL00138 21 ENKWEERVIQIKRVSKVVKGGKKLSFRAIVVIGNENGWVGVGVGKADDVQNAVKKAVT 78 (143)
T ss_pred CCCceEEEEEEeeeeEEecCCcEEEEEEEEEEECCCCeEEEeeEecchHHHHHHHHHH
Confidence 5789999999999999999999999999999999999999999999999999999975
No 9
>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=99.74 E-value=1.9e-18 Score=154.30 Aligned_cols=56 Identities=38% Similarity=0.605 Sum_probs=54.3
Q ss_pred CcceeeeEeecceeeccCCeeEEEEEEEEEecCCCceeeeeccCCcHHHHhhhhcC
Q 013474 387 GFDVKLIDVNRTCKVTKGGQVVKYTAMLACGNYHGVVGFAKAKGPAVPIALQKVTW 442 (442)
Q Consensus 387 ~LkEeVLdInRVQKmTKgGRRtRFrALVVVGNgNG~VGlGvGKAKEVatAIrKAIW 442 (442)
+|+++||+|+||||||++||+++|+|||||||+||+||||+|||+|+++||+||++
T Consensus 1 ~l~e~vl~i~rv~k~tkgGr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~kA~~ 56 (154)
T TIGR01021 1 ELEERLIAVNRVSKVVKGGRRFSFSALVVVGDGKGRVGFGFGKAKEVPDAIKKAVE 56 (154)
T ss_pred CceeEEEEEeeeeEEecCCcEEEEEEEEEEECCCCeEeeeeeecchHHHHHHHHHH
Confidence 48899999999999999999999999999999999999999999999999999975
No 10
>PRK00550 rpsE 30S ribosomal protein S5; Validated
Probab=99.72 E-value=5.8e-18 Score=153.19 Aligned_cols=58 Identities=33% Similarity=0.579 Sum_probs=55.9
Q ss_pred cCCcceeeeEeecceeeccCCeeEEEEEEEEEecCCCceeeeeccCCcHHHHhhhhcC
Q 013474 385 RKGFDVKLIDVNRTCKVTKGGQVVKYTAMLACGNYHGVVGFAKAKGPAVPIALQKVTW 442 (442)
Q Consensus 385 lp~LkEeVLdInRVQKmTKgGRRtRFrALVVVGNgNG~VGlGvGKAKEVatAIrKAIW 442 (442)
..+|+++||+|+||||||++||+++|+|||||||+||+||||+|||+|+++||+||+|
T Consensus 10 ~~~l~~~vl~v~rv~k~tk~Gr~~~f~alvvvGn~~G~vG~G~gKa~ev~~Ai~kA~~ 67 (168)
T PRK00550 10 KLELEEKVVAINRVTKVVKGGRRFSFSALVVVGDGKGRVGFGYGKAREVPEAIRKAVE 67 (168)
T ss_pred cCCceEEEEEEeeeEEEecCCcEEEEEEEEEEECCCCeEeeeeeecchHHHHHHHHHH
Confidence 3489999999999999999999999999999999999999999999999999999985
No 11
>KOG2646 consensus Ribosomal protein S5 [Translation, ribosomal structure and biogenesis]
Probab=98.60 E-value=1.1e-08 Score=103.25 Aligned_cols=57 Identities=19% Similarity=0.380 Sum_probs=50.8
Q ss_pred CCcceeeeEe--ecceeeccCCeeEEEEEEEEEecCCCceeeeeccCC-cHHHHhhhhcC
Q 013474 386 KGFDVKLIDV--NRTCKVTKGGQVVKYTAMLACGNYHGVVGFAKAKGP-AVPIALQKVTW 442 (442)
Q Consensus 386 p~LkEeVLdI--nRVQKmTKgGRRtRFrALVVVGNgNG~VGlGvGKAK-EVatAIrKAIW 442 (442)
.+|+.+++.+ ++|..||+.|++.+|.|||||||+||.+|||.|||. .-..||.+|+|
T Consensus 180 ~Dfe~r~l~lvrr~~~~~~r~Gki~s~~~LVvvGn~nGaaG~~eGKa~~~~s~A~~ka~~ 239 (396)
T KOG2646|consen 180 LDFELRHLELVRRRVENQNRKGKIASMYALVVVGNGNGAAGLGEGKAADPNSPAIYKAIG 239 (396)
T ss_pred hhhhHHHHHHHHhhhhccccccceeeEEEEEEEecCCcceeeccccCcCccCHHHHHHHH
Confidence 3667777777 567778889999999999999999999999999999 78899999998
No 12
>KOG0772 consensus Uncharacterized conserved protein, contains WD40 repeat [Function unknown]
Probab=70.06 E-value=1.7 Score=47.37 Aligned_cols=18 Identities=56% Similarity=0.962 Sum_probs=12.9
Q ss_pred cCCCcccccccccchhHHHH
Q 013474 132 KDIDQEDEEDYMGVGPLIEK 151 (442)
Q Consensus 132 ~d~d~e~eedy~gv~pliek 151 (442)
.|..+|||||+|| ||=-+
T Consensus 99 ~e~~de~ee~~mg--plPP~ 116 (641)
T KOG0772|consen 99 DEEEDEDEEDFMG--PLPPK 116 (641)
T ss_pred ccccccchhhhcC--CCCch
Confidence 4556788999999 65444
No 13
>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=63.99 E-value=22 Score=33.68 Aligned_cols=105 Identities=20% Similarity=0.168 Sum_probs=65.3
Q ss_pred hhhhHHHhhhcCCCCCCChHHhhhhhhhhhHHHHHHHhHhHhhhhhhhhhHHhhccCCccchHHHHHHHHHhhhhhhhcc
Q 013474 301 AEMDEEKRLLQGGVDDDDEEEFDDMKERDDILLERLNAIDKKLEEKLAELDHTFGKKGKLLEEEIRDLAEERNALTEKKR 380 (442)
Q Consensus 301 a~~~~ek~~~~g~~d~~~eeEf~d~kEkd~i~itKLg~ivKk~EGKI~sLdeiF~k~~pIlE~EIVD~LeerN~Ltekkr 380 (442)
+|...|.-+++| ..+.-|||-..+..++++ ....|+ .-....-++|.+.++.-.
T Consensus 116 ~g~s~~eA~~~a---------l~E~iERda~~~~w~~~~------~~~~i~----~~~~~~~~~~~~~~~~~~------- 169 (332)
T PF02624_consen 116 AGNSLEEAILHA---------LLEVIERDAFSLWWYNRL------PPPRID----DVLDPTLPELLERLERLR------- 169 (332)
T ss_pred CCCCHHHHHHHH---------HHHHHHHHHHHHHHHhcC------CCCeEe----cccCcCCHHHHHHHHHhh-------
Confidence 355555555555 578899999999998886 222333 223355667777771100
Q ss_pred cccccCCcceeeeEeecceeeccCCeeEEEEEEE-EEecCCCceeeeeccCCcHHHHhhhhc
Q 013474 381 RPLYRKGFDVKLIDVNRTCKVTKGGQVVKYTAML-ACGNYHGVVGFAKAKGPAVPIALQKVT 441 (442)
Q Consensus 381 ~p~~lp~LkEeVLdInRVQKmTKgGRRtRFrALV-VVGNgNG~VGlGvGKAKEVatAIrKAI 441 (442)
..++.-.+++| |.......|-|++ ......+.+.+|.|++.....|+.+|+
T Consensus 170 ----~~~~~v~l~di------t~~~~vpv~~a~~~~~~~~~~~~~~G~ga~~~~~~Al~rAl 221 (332)
T PF02624_consen 170 ----EAGLEVRLFDI------TNDFGVPVVAAVLRNEDKDRPYYAVGAGAHLDPEEALERAL 221 (332)
T ss_pred ----cCceEEEEEEC------CCCCCceEEEEEEEecCCCCcceEEEeccCCCHHHHHHHHH
Confidence 12455566666 4444333333333 123667778999999999999999985
No 14
>PF08031 BBE: Berberine and berberine like ; InterPro: IPR012951 This domain is found in the berberine bridge and berberine bridge-like enzymes, which are involved in the biosynthesis of numerous isoquinoline alkaloids. They catalyse the transformation of the N-methyl group of (S)-reticuline into the C-8 berberine bridge carbon of (S)-scoulerine [].; GO: 0016491 oxidoreductase activity, 0050660 flavin adenine dinucleotide binding, 0055114 oxidation-reduction process; PDB: 2IPI_A 2Y3S_A 2Y3R_D 2Y08_B 2Y4G_A 3D2H_A 3FW9_A 3FW8_A 3FWA_A 3D2J_A ....
Probab=59.99 E-value=3.7 Score=30.44 Aligned_cols=15 Identities=47% Similarity=0.616 Sum_probs=11.6
Q ss_pred HhhhhhhhhccCCCC
Q 013474 265 AMRLVEWKEVYDPNN 279 (442)
Q Consensus 265 a~rl~e~keaydp~n 279 (442)
.=||++-|..|||+|
T Consensus 24 ~~rL~~iK~~yDP~n 38 (47)
T PF08031_consen 24 YDRLRAIKRKYDPDN 38 (47)
T ss_dssp HHHHHHHHHHH-TT-
T ss_pred HHHHHHHHHHhCccc
Confidence 458999999999997
No 15
>PF04979 IPP-2: Protein phosphatase inhibitor 2 (IPP-2); InterPro: IPR007062 Protein phosphatase inhibitor 2 (IPP-2) is a phosphoprotein conserved among all eukaryotes, and it appears in both the nucleus and cytoplasm of tissue culture cells [].; GO: 0004864 protein phosphatase inhibitor activity, 0009966 regulation of signal transduction, 0043666 regulation of phosphoprotein phosphatase activity; PDB: 2O8G_I 2O8A_J.
Probab=53.95 E-value=9.1 Score=32.46 Aligned_cols=57 Identities=28% Similarity=0.433 Sum_probs=13.4
Q ss_pred cccccchhHHHHHHHhhhcccCCCCCccCCCCCCCchhhcccChHHHHHhHHHHHHHHHhHH
Q 013474 140 EDYMGVGPLIEKLEKERLKDTGDLNLYEEPTDSDSDEDDERFSRDAVNKRFQVFQKKFKRHK 201 (442)
Q Consensus 140 edy~gv~plieklek~~~k~~~~~~~~~e~tdsdsd~d~e~~~~d~~~kr~~~f~~k~~rh~ 201 (442)
.+-+...-|.++| ...........+...+++++++++ + ....+.|-..|+++.|.|-
T Consensus 50 ~~~vd~e~L~e~l---~a~~~~~~~~~~~~~~~~~~~~~~-~-~~e~~~k~~~Fee~RK~HY 106 (132)
T PF04979_consen 50 EDSVDPEELAEKL---AASDSSEPSVSWEDSEDDEDEEEE-L-TEEEKEKHREFEEKRKAHY 106 (132)
T ss_dssp --------------------------------------------TTHHHHHHHHHHHHHHH-
T ss_pred cccccHHHHHHHH---hhhccccccccccccccccccccc-c-chhhHHHHHHHHHHHHHHh
Confidence 3444455577888 222333344444444444433333 3 3444667778999999996
No 16
>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]
Probab=45.79 E-value=41 Score=36.59 Aligned_cols=92 Identities=24% Similarity=0.399 Sum_probs=52.5
Q ss_pred HHHHHHhHHHHHHHHcCCCCcCCCcccccccccchhHHHHHHHhhhc---ccCCCCCccCCCCCCCc----hhhcccChH
Q 013474 112 EVEREKGREREARKRQGLDTKDIDQEDEEDYMGVGPLIEKLEKERLK---DTGDLNLYEEPTDSDSD----EDDERFSRD 184 (442)
Q Consensus 112 evere~~rer~~r~r~g~d~~d~d~e~eedy~gv~plieklek~~~k---~~~~~~~~~e~tdsdsd----~d~e~~~~d 184 (442)
+++|++|+++ ..+.++|+.+||+-.-|+-++.++-..| ..+....-++..||.|. +||-- ++.
T Consensus 3 ~~~r~r~~~~---------~se~~de~d~dyv~yv~v~err~~~~~k~l~r~~k~~~~~~q~~~~~~~~~~~~d~~-g~~ 72 (610)
T KOG0341|consen 3 DRRRKRQEEE---------DSEGDDEDDEDYVPYVPVQERRAQVHRKLLQRQVKAPTEEEQEDSESEREKKEDDKQ-GEE 72 (610)
T ss_pred chhhhhhhhh---------cccccccccccceecccHHHHHHHHHHHHHHhhccccchhhccchhcccccCccccc-chh
Confidence 4556666555 2566778888999999998887654333 23334344444444432 12111 222
Q ss_pred HHH--------------HhHHHHHHHHHhHHHHHHhhhhcCCh
Q 013474 185 AVN--------------KRFQVFQKKFKRHKELLQNFTEAETP 213 (442)
Q Consensus 185 ~~~--------------kr~~~f~~k~~rh~ell~~f~~aetl 213 (442)
+.+ .+++.-++.....++++.+.++..+|
T Consensus 73 ~n~sLL~qh~elk~~~~ak~sa~Ekql~eEee~me~v~~~k~L 115 (610)
T KOG0341|consen 73 ANKSLLDQHTELKETAEAKISASEKQLMEEEEIMESVADGKAL 115 (610)
T ss_pred hhhhHHHHHHHHHhhhhhhcchHHHHHHHHHHHHHHHhcCccc
Confidence 221 14555667777778888777665544
No 17
>PF11802 CENP-K: Centromere-associated protein K; InterPro: IPR020993 Cenp-K is one of seven new Cenp-A-nucleosome distal (CAD) centromere components (the others being Cenp-L, Cenp-O, Cenp-P, Cenp-Q, Cenp-R and Cenp-S) that are identified as assembling on the Cenp-A nucleosome associated complex, NAC []. The Cenp-A NAC is essential, as disruption of the complex causes errors of chromosome alignment and segregation that preclude cell survival despite continued centromere-derived mitotic checkpoint signalling. Cenp-K is centromere-associated through its interaction with one or more components of the Cenp-A NAC.; GO: 0005634 nucleus
Probab=38.36 E-value=29 Score=35.08 Aligned_cols=39 Identities=31% Similarity=0.617 Sum_probs=31.1
Q ss_pred HHhhhhhhhhhccCCCCch---------------------hhHHHHHHHHhHhhhccchhH
Q 013474 218 KWMNKIDKFEQKHFPLRHE---------------------YRVIGELMNRLKEAEGKDKFM 257 (442)
Q Consensus 218 k~m~kid~fe~kh~~l~~e---------------------yrvig~lmnrlk~aegkd~f~ 257 (442)
+.|..++.|=++||+|+.+ +-+|-.|||||=.+.| |-||
T Consensus 172 ~Ll~~LgeFLeeHfPlp~~~~~~~Kkk~~~~e~~~~~~~l~eilE~LmN~l~~~p~-DpYv 231 (268)
T PF11802_consen 172 KLLSFLGEFLEEHFPLPDEQGNAKKKKKGEDEPSAQLITLREILEILMNKLLDSPH-DPYV 231 (268)
T ss_pred HHHHHHHHHHHhcCCCCcccchhhhhhccccccchhhhHHHHHHHHHHHHhcCCCC-CCce
Confidence 4688899999999999987 6678888888877665 4554
No 18
>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=38.33 E-value=39 Score=24.14 Aligned_cols=28 Identities=11% Similarity=0.243 Sum_probs=20.2
Q ss_pred CCeeEEEEEEEEEecCCCceeeeeccCCcH
Q 013474 404 GGQVVKYTAMLACGNYHGVVGFAKAKGPAV 433 (442)
Q Consensus 404 gGRRtRFrALVVVGNgNG~VGlGvGKAKEV 433 (442)
.+....|.+.|.|++ -.++-|.|+++..
T Consensus 28 ~~~~~~f~~~v~i~~--~~~~~g~g~sKk~ 55 (68)
T cd00048 28 PDHAPRFTVEVTVGG--KITGEGEGSSKKE 55 (68)
T ss_pred CCCCCeEEEEEEECC--EEEEEeecCCHHH
Confidence 344578999999975 4778888876654
No 19
>smart00358 DSRM Double-stranded RNA binding motif.
Probab=36.68 E-value=31 Score=24.88 Aligned_cols=28 Identities=11% Similarity=0.202 Sum_probs=19.0
Q ss_pred CeeEEEEEEEEEecCCCceeeeeccCCcHH
Q 013474 405 GQVVKYTAMLACGNYHGVVGFAKAKGPAVP 434 (442)
Q Consensus 405 GRRtRFrALVVVGNgNG~VGlGvGKAKEVa 434 (442)
+....|.+-|.|++. .+|-|.|+++..+
T Consensus 27 ~~~~~f~~~v~i~~~--~~~~g~g~sKk~A 54 (67)
T smart00358 27 DHAPRFTVTVKVGGE--YTGEGEGSSKKEA 54 (67)
T ss_pred CCCCcEEEEEEECCE--EEEEeccCCHHHH
Confidence 444589999998643 6777777766533
No 20
>PF05553 DUF761: Cotton fibre expressed protein; InterPro: IPR008480 This family consists of several plant proteins of unknown function. Three of the sequences from Gossypium hirsutum (Upland cotton) in this family are described as G. hirsutum fibre expressed proteins []. The remaining sequences, found in Arabidopsis thaliana, are uncharacterised.
Probab=34.16 E-value=52 Score=24.49 Aligned_cols=21 Identities=33% Similarity=0.578 Sum_probs=17.5
Q ss_pred hHHHHHhHHHHHHHHHhHHHH
Q 013474 183 RDAVNKRFQVFQKKFKRHKEL 203 (442)
Q Consensus 183 ~d~~~kr~~~f~~k~~rh~el 203 (442)
-+.|++|.+.|..+|.+|-.|
T Consensus 2 ~~evd~rAe~FI~~f~~qlrl 22 (38)
T PF05553_consen 2 DDEVDRRAEEFIAKFREQLRL 22 (38)
T ss_pred chHHHHHHHHHHHHHHHHHHH
Confidence 367899999999999887654
No 21
>KOG1945 consensus Protein phosphatase 1 binding protein spinophilin/neurabin II [Signal transduction mechanisms]
Probab=33.90 E-value=28 Score=36.68 Aligned_cols=61 Identities=26% Similarity=0.384 Sum_probs=35.8
Q ss_pred cccccccCCCCccCCC---CCCCCCCCCCCCCCcccccccccccccccccccccc---ccccCCCCccccccccc
Q 013474 28 SFSRKISTFPHFLTNQ---TPPNPLPPRTHFPNASQEYSAKPIYSFSRKISTFSH---FRYNQTSKPSILLKSHF 96 (442)
Q Consensus 28 ~~~~~~~~~~~f~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~f 96 (442)
.++-+.+.||.||+.. .||.|||||... ..|.+-.|--+|.|+- .+-|+++.|++...-++
T Consensus 24 ~~~er~~~~~s~~~p~~q~~ppp~~p~~~~~--------~~~~~~~s~v~sa~~ve~~~~~n~~t~~~a~~~~~e 90 (377)
T KOG1945|consen 24 EQLERQQDVPSFYSPRLQRQPPPPLPPKPPS--------QCPPSPMSQVFSAFSVEDYDRKNEDTDPVASCAEYE 90 (377)
T ss_pred HHHHHhhccCCcCCcccCCCCCCCCCCCccc--------cCCCcchhhhhhhhhhhhccccCCCccccccCCccc
Confidence 3456778888887643 355577777654 2333333334444443 35588888877654443
No 22
>TIGR03604 docking_ocin bacteriocin biosynthesis docking scaffold, SagD family. prokaryotic systems for making a general class of heterocycle-containing bacteriocins.
Probab=32.13 E-value=1.3e+02 Score=30.25 Aligned_cols=105 Identities=24% Similarity=0.284 Sum_probs=66.2
Q ss_pred hhhhhHHHhhhcCCCCCCChHHhhhhhhhhhHHHHHHHhHhHhhhhhhhhhHHhhccCCccchHHHHHHHHHhhhhhhhc
Q 013474 300 NAEMDEEKRLLQGGVDDDDEEEFDDMKERDDILLERLNAIDKKLEEKLAELDHTFGKKGKLLEEEIRDLAEERNALTEKK 379 (442)
Q Consensus 300 ~a~~~~ek~~~~g~~d~~~eeEf~d~kEkd~i~itKLg~ivKk~EGKI~sLdeiF~k~~pIlE~EIVD~LeerN~Ltekk 379 (442)
-+|..-|+-..+| .-++-|||-+.+..++++ .+..|+-- + .-++|..++. .+ .
T Consensus 117 A~G~s~~eAi~~g---------l~EvIERDa~~~~w~~~~------~~~~Id~~-~-----~~~~~~~l~~---~~---~ 169 (377)
T TIGR03604 117 AAGETLEEAILNG---------LLEVIERDAFMLTWYGRL------PLPRIDVD-S-----EDPEIRLLVA---RL---G 169 (377)
T ss_pred cCCCCHHHHHHHH---------HHHHHHHHHHHHHHhcCC------CCCccCcc-c-----CCHHHHHHHH---HH---h
Confidence 3577777777777 578899999999998876 22222211 1 1244544441 01 0
Q ss_pred ccccccCCcceeeeEeecceeeccCCeeEEEEEEEEEecC-CCceeeeeccCCcHHHHhhhhc
Q 013474 380 RRPLYRKGFDVKLIDVNRTCKVTKGGQVVKYTAMLACGNY-HGVVGFAKAKGPAVPIALQKVT 441 (442)
Q Consensus 380 r~p~~lp~LkEeVLdInRVQKmTKgGRRtRFrALVVVGNg-NG~VGlGvGKAKEVatAIrKAI 441 (442)
...++.-.++++ |....+..|-|++.-.+. .+.+-+|.|++.....|+.+|+
T Consensus 170 ----~~~g~~v~l~d~------t~d~~vPvv~a~~~~~~~~~~~~~~G~g~~~~~~~A~~rAl 222 (377)
T TIGR03604 170 ----KLTGYEVHLLDI------TTDLGIPVVGALAKNPDDALPLLVFGAGAHLDPEKALKKAL 222 (377)
T ss_pred ----hcCCceEEEEec------ccCCCCCEEEEEEEccCCCCcceEEEecCCCCHHHHHHHHH
Confidence 023566677776 545566677666654332 3457789999999999999986
No 23
>PF03656 Pam16: Pam16; InterPro: IPR005341 The Pam16 protein is the fifth essential subunit of the pre-sequence translocase-associated protein import motor (PAM) []. In Saccharomyces cerevisiae (Baker's yeast), Pam16 is required for preprotein translocation into the matrix, but not for protein insertion into the inner membrane [].; PDB: 2GUZ_J.
Probab=29.09 E-value=1.3e+02 Score=27.25 Aligned_cols=49 Identities=35% Similarity=0.399 Sum_probs=28.5
Q ss_pred cCChhHHHHHhhhhhhhhhccCCCCchhhHHHHHHHH---hHhhhccc---hhHHHHHHHhHhhhhh
Q 013474 210 AETPDEAFKWMNKIDKFEQKHFPLRHEYRVIGELMNR---LKEAEGKD---KFMLQQKLNRAMRLVE 270 (442)
Q Consensus 210 aetld~a~k~m~kid~fe~kh~~l~~eyrvig~lmnr---lk~aegkd---~f~l~~klnra~rl~e 270 (442)
-=|||||.+.+| +++ .+. ..++++| |=.+.-|+ -|.||.|++||--.++
T Consensus 54 ~Mtl~EA~~ILn-v~~------~~~-----~eeI~k~y~~Lf~~Nd~~kGGSfYLQSKV~rAKErl~ 108 (127)
T PF03656_consen 54 GMTLDEARQILN-VKE------ELS-----REEIQKRYKHLFKANDPSKGGSFYLQSKVFRAKERLE 108 (127)
T ss_dssp ---HHHHHHHHT---G--------S-----HHHHHHHHHHHHHHT-CCCTS-HHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHcC-CCC------ccC-----HHHHHHHHHHHHhccCCCcCCCHHHHHHHHHHHHHHH
Confidence 368999998877 444 333 3344444 44566664 7999999999986555
No 24
>PF07710 P53_tetramer: P53 tetramerisation motif; InterPro: IPR010991 The p53 protein is a tetrameric transcription factor that plays a central role in the prevention of neoplastic transformation []. Oligomerization appears to be essential for the tumour suppressing activity of p53. p53 can be divided into different functional domains: an N-terminal transactivation domain, a proline-rich domain, a DNA-binding domain (IPR008967 from INTERPRO), a tetramerisation domain and a C-terminal regulatory region. The tetramerisation domain of human p53 extends from residues 325 to 356, and has a 4-helical bundle fold. The tetramerisation domain is essential for DNA binding, protein-protein interactions, post-translational modifications, and p53 degradation [].; GO: 0051262 protein tetramerization; PDB: 3Q06_B 1SAL_B 1OLH_B 1AIE_A 1PES_D 1SAK_D 1SAE_B 2J11_D 1PET_A 1OLG_A ....
Probab=27.38 E-value=45 Score=25.43 Aligned_cols=22 Identities=23% Similarity=0.602 Sum_probs=19.5
Q ss_pred hccchhHHHHHHHhHhhhhhhh
Q 013474 251 EGKDKFMLQQKLNRAMRLVEWK 272 (442)
Q Consensus 251 egkd~f~l~~klnra~rl~e~k 272 (442)
-|+++|-+..|||-|+-|++-.
T Consensus 16 rGRe~yE~l~kine~LEL~d~~ 37 (42)
T PF07710_consen 16 RGRERYEMLKKINEALELMDAV 37 (42)
T ss_dssp ESHHHHHHHHHHHHHHHHHGGS
T ss_pred ecHHHHHHHHHHHHHHHHHhhc
Confidence 4899999999999999998753
No 25
>TIGR00702 uncharacterized domain. This uncharacterized domain comprises the whole of a protein in 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=23.67 E-value=1.3e+02 Score=30.61 Aligned_cols=104 Identities=17% Similarity=0.266 Sum_probs=65.1
Q ss_pred hhhhhHHHhhhcCCCCCCChHHhhhhhhhhhHHHHHHHhHhHhhhhhhhhhHHhhccCCccchHHHHHHHHHhhhhhhhc
Q 013474 300 NAEMDEEKRLLQGGVDDDDEEEFDDMKERDDILLERLNAIDKKLEEKLAELDHTFGKKGKLLEEEIRDLAEERNALTEKK 379 (442)
Q Consensus 300 ~a~~~~ek~~~~g~~d~~~eeEf~d~kEkd~i~itKLg~ivKk~EGKI~sLdeiF~k~~pIlE~EIVD~LeerN~Ltekk 379 (442)
-+|...|.-..|| .-+.=|||-.-|....++-. . .| .++... +-.-.++++.+
T Consensus 159 AaGnt~eEAi~~g---------L~EvIERDa~~i~~~~~~~~-~--~i-~~~~~~----~~~~~~l~~~~---------- 211 (377)
T TIGR00702 159 ASGNTRDEAILHG---------LSEVIERDAWSLAEAARLPE-I--EV-DVDDRY----NSIIAHLIEKL---------- 211 (377)
T ss_pred CCCCCHHHHHHHH---------HHHHHHHHHHHHHhhccCCC-C--Cc-cccccC----CHHHHHHHHHH----------
Confidence 3677888888888 56788888887766554411 1 00 000100 01112233333
Q ss_pred ccccccCCcceeeeEeecceeeccCCeeEEEEEEEEEecCCCceeeeeccCCcHHHHhhhhc
Q 013474 380 RRPLYRKGFDVKLIDVNRTCKVTKGGQVVKYTAMLACGNYHGVVGFAKAKGPAVPIALQKVT 441 (442)
Q Consensus 380 r~p~~lp~LkEeVLdInRVQKmTKgGRRtRFrALVVVGNgNG~VGlGvGKAKEVatAIrKAI 441 (442)
...++.-.++++ |..+..-.|-|++. .-.+|.+.+|.|++.....|+.+|+
T Consensus 212 ----~~~G~~v~l~D~------t~d~giPvv~a~~~-~~~~~~~~~g~Gah~~~~~Al~RAL 262 (377)
T TIGR00702 212 ----EAAGVPIDLADL------TLGGGYPVVAAVLD-DPTLGTLFGGFGAHLDPEVALERAL 262 (377)
T ss_pred ----HhCCCeEEEEEC------cCCCCceEEEEEEE-CCCCCceeEEeccCCCHHHHHHHHH
Confidence 123666777777 77777888866554 3246889999999999999999985
No 26
>PF15463 ECM11: Extracellular mutant protein 11
Probab=21.84 E-value=3.5e+02 Score=24.12 Aligned_cols=56 Identities=29% Similarity=0.436 Sum_probs=38.5
Q ss_pred CCCChHHhhhhhhhhhH-----HHHHHHhHhHhhhhhhhhhHHhhccCCccchHHHHHHHHHhhh
Q 013474 315 DDDDEEEFDDMKERDDI-----LLERLNAIDKKLEEKLAELDHTFGKKGKLLEEEIRDLAEERNA 374 (442)
Q Consensus 315 d~~~eeEf~d~kEkd~i-----~itKLg~ivKk~EGKI~sLdeiF~k~~pIlE~EIVD~LeerN~ 374 (442)
+.+.+.-|..|.-.+|+ ++.+-+.|..+|...-..+-..|. +.|.+|.+..+..+.
T Consensus 59 ~~~q~~~fs~ls~~eWe~~Gd~~l~qf~~l~~kl~~~R~~~r~~~~----~fe~eI~~R~eav~~ 119 (139)
T PF15463_consen 59 EQEQEEFFSNLSFDEWEEAGDWFLEQFSELMQKLKEARRKLRKKFA----VFEDEINRRAEAVRA 119 (139)
T ss_pred hHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHH
Confidence 44445667777777776 788888888877655556666666 677888777655544
No 27
>KOG3228 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.39 E-value=8.4e+02 Score=24.51 Aligned_cols=25 Identities=24% Similarity=0.226 Sum_probs=12.1
Q ss_pred ccccccccCccchHHHHHHHHHHHH
Q 013474 91 LLKSHFSTGSAYSRVAQDLLAEVER 115 (442)
Q Consensus 91 ~~~~~fs~~~~~~~v~~~ll~ever 115 (442)
|.++-++.+.+.+---++|-+|+|+
T Consensus 41 lKyRq~~Q~teee~rk~dlR~elee 65 (226)
T KOG3228|consen 41 LKYRQTGQGTEEELRKRDLRRELEE 65 (226)
T ss_pred cchhhcccccHHHHHHHHHHHHHHH
Confidence 3444455443333334556666653
No 28
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=20.70 E-value=76 Score=26.63 Aligned_cols=38 Identities=24% Similarity=0.379 Sum_probs=31.4
Q ss_pred HHHHHhHhhhccchhHHHHHHHhHhhhhhhhh----ccCCCCCC
Q 013474 242 ELMNRLKEAEGKDKFMLQQKLNRAMRLVEWKE----VYDPNNPT 281 (442)
Q Consensus 242 ~lmnrlk~aegkd~f~l~~klnra~rl~e~ke----aydp~npa 281 (442)
-=+++|+ .||.++|=.+-|++-.+-.+|+- .|+|++..
T Consensus 30 ~~ls~l~--~gk~k~I~~~tL~~iC~~LeCqpgDiley~~d~~~ 71 (73)
T COG3655 30 ANLSKLK--TGKVKAIRLSTLEKICKALECQPGDILEYVPDSDD 71 (73)
T ss_pred HHHHHHH--cCCcceeeHHHHHHHHHHcCCChhheeEEecCCcc
Confidence 3467787 99999999999999999999985 47777654
No 29
>PF14131 DUF4298: Domain of unknown function (DUF4298)
Probab=20.38 E-value=1.3e+02 Score=25.24 Aligned_cols=21 Identities=33% Similarity=0.529 Sum_probs=12.3
Q ss_pred hHHHHHHHHHhHHHHHHhhhh
Q 013474 189 RFQVFQKKFKRHKELLQNFTE 209 (442)
Q Consensus 189 r~~~f~~k~~rh~ell~~f~~ 209 (442)
|++..++++.++.++|..+.+
T Consensus 1 rI~eme~~y~~~~~~l~~le~ 21 (90)
T PF14131_consen 1 RIQEMEKIYNEWCELLEELEE 21 (90)
T ss_pred CHHHHHHHHHHHHHHHHHHHH
Confidence 455566666666666655544
No 30
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=20.35 E-value=2.1e+02 Score=31.86 Aligned_cols=12 Identities=25% Similarity=0.127 Sum_probs=6.0
Q ss_pred hHHHHHHHHHHH
Q 013474 103 SRVAQDLLAEVE 114 (442)
Q Consensus 103 ~~v~~~ll~eve 114 (442)
..-++-||.=++
T Consensus 622 ~~~l~~ll~vl~ 633 (784)
T PF04931_consen 622 ESGLQLLLDVLD 633 (784)
T ss_pred HHHHHHHHHHhc
Confidence 344555555554
No 31
>PF04450 BSP: Peptidase of plants and bacteria; InterPro: IPR007541 These basic secretory proteins (BSPs) are believed to be part of the plants defence mechanism against pathogens [].
Probab=20.30 E-value=95 Score=29.65 Aligned_cols=94 Identities=19% Similarity=0.260 Sum_probs=53.1
Q ss_pred CCchhhcccChHHHHHhHHH--HHH---HHHhHH--HHHHhhhh-------cCChhHHHHHhhhhhhhhhccCCCC----
Q 013474 173 DSDEDDERFSRDAVNKRFQV--FQK---KFKRHK--ELLQNFTE-------AETPDEAFKWMNKIDKFEQKHFPLR---- 234 (442)
Q Consensus 173 dsd~d~e~~~~d~~~kr~~~--f~~---k~~rh~--ell~~f~~-------aetld~a~k~m~kid~fe~kh~~l~---- 234 (442)
|+++....||++-+.+-... ... --=.|+ -+.|.... -|-.-|..+... .|..-|-+.+
T Consensus 70 d~~~~~I~~S~~~i~~~~~~~~~~~Ei~Gvl~HE~~H~~Q~~~~~~~P~~liEGIADyVRl~a---G~~~~~w~~p~~~~ 146 (205)
T PF04450_consen 70 DDDHKEIHFSARYIAKYPADGDVRDEIIGVLYHEMVHCWQWDGRGTAPGGLIEGIADYVRLKA---GYAPPHWKRPGGGD 146 (205)
T ss_pred CCCccEEEEeHHHHhhcccccchHHHHHHHHHHHHHHHhhcCCCCCCChhheecHHHHHHHHc---CCCCccccCCCCCC
Confidence 66667788888777665421 100 001121 12232222 133445544443 3344555543
Q ss_pred ---chhhHHHHHHHHhHhhhccchhHHHHHHHhHhhhhhh
Q 013474 235 ---HEYRVIGELMNRLKEAEGKDKFMLQQKLNRAMRLVEW 271 (442)
Q Consensus 235 ---~eyrvig~lmnrlk~aegkd~f~l~~klnra~rl~e~ 271 (442)
.-|++-|-.++=|....-+.-|| +|||+|||-..|
T Consensus 147 ~wd~gY~~TA~FL~wle~~~~~~gfV--~~LN~~m~~~~y 184 (205)
T PF04450_consen 147 SWDDGYRTTARFLDWLEDNRYGKGFV--RRLNEAMRRDKY 184 (205)
T ss_pred CcccccHHHHHHHHHHHhcccCccHH--HHHHHHHhhCCC
Confidence 46999999999998733334455 799999987777
Done!