Query 022215
Match_columns 301
No_of_seqs 161 out of 195
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 08:53:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022215.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022215hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3068 mRNA splicing factor [ 100.0 1.3E-93 2.9E-98 652.4 18.3 267 1-283 1-268 (268)
2 PF06246 Isy1: Isy1-like splic 100.0 1E-88 2.3E-93 629.8 7.5 249 1-281 1-255 (255)
3 PF10453 NUFIP1: Nuclear fragi 56.1 10 0.00022 28.5 2.3 21 255-275 13-33 (56)
4 cd00319 Ribosomal_S12_like Rib 45.6 7.7 0.00017 32.2 0.3 11 131-141 70-80 (95)
5 KOG1918 3-methyladenine DNA gl 29.7 33 0.00072 32.8 1.8 131 7-157 92-233 (254)
6 KOG1513 Nuclear helicase MOP-3 26.0 1.1E+02 0.0024 34.6 5.1 69 39-134 769-837 (1300)
7 PF10296 DUF2404: Putative int 25.8 32 0.00069 27.1 0.8 36 40-75 11-47 (91)
8 CHL00051 rps12 ribosomal prote 25.5 26 0.00056 30.4 0.3 13 131-143 85-97 (123)
9 COG3890 ERG8 Phosphomevalonate 22.7 1.6E+02 0.0034 29.4 5.0 91 40-141 210-312 (337)
10 cd03368 Ribosomal_S12 S12-like 22.4 31 0.00068 29.2 0.2 11 131-141 83-93 (108)
11 PRK05163 rpsL 30S ribosomal pr 22.4 32 0.0007 29.8 0.3 13 131-143 85-97 (124)
12 TIGR00981 rpsL_bact ribosomal 22.2 32 0.0007 29.8 0.2 13 131-143 85-97 (124)
13 TIGR03504 FimV_Cterm FimV C-te 21.4 67 0.0014 22.7 1.7 23 276-298 20-42 (44)
14 PF00164 Ribosom_S12_S23: Ribo 21.0 40 0.00086 29.1 0.5 17 128-144 81-97 (122)
No 1
>KOG3068 consensus mRNA splicing factor [RNA processing and modification]
Probab=100.00 E-value=1.3e-93 Score=652.35 Aligned_cols=267 Identities=58% Similarity=0.904 Sum_probs=232.8
Q ss_pred CCCcHHhHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCChHHHHHHHHHHHHHHHHhHHHHhhcCCCcchhhhchHHHHH
Q 022215 1 MARNEEKAQSMLNRYIALQAEEKKKPKERRPYLASECRDLSEADKWRQQIMREIGRKVAEIQNEGLGEHRLRDLNDEINK 80 (301)
Q Consensus 1 MARN~EKA~smL~R~~~~k~~e~~~~~~rRP~~~s~v~~l~~aekWR~~Ii~EIs~kv~~Iqd~~L~E~~IRDLNDeINk 80 (301)
||||+|||||||+||+++|.+++++++.+||+++|+|+||++|++||+||++|||+||++||||+||||+||||||+||+
T Consensus 1 MaRN~eka~t~LaRf~~~k~ee~~~pkerRP~~~sec~~l~~aekwRrqIvreIskKva~Iqn~gLgE~rirDLNDEiNk 80 (268)
T KOG3068|consen 1 MARNAEKAMTALARFREAKEEEGGKPKERRPYLASECKSLPEAEKWRRQIVREISKKVARIQNAGLGEFRIRDLNDEINK 80 (268)
T ss_pred CCccHHHHHHHHHHHHHHHHHhccCccccCcccHHhhcccHHHHHHHHHHHHHHHHHHHHHhcCCcchhhhHHHHHHHHH
Confidence 99999999999999999999999889999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhchHHHHHHhcCCCCccccccccccCCCcccCCCCCCCCCCceeeeccccCchhhhhhcCCch-hhhhcchHHHh
Q 022215 81 LIREKGHWERRIFELGGPNYTKHFAKMTDLEGNIVDVPNPSGRGPGYRYFGAAKKLPGVRELFEKPPE-LRKRRTRYDIY 159 (301)
Q Consensus 81 L~rEK~~WE~rI~eLGGpdY~~~~~k~~d~~G~~~evpg~~g~~~GYrYFGrAKeLPgVkELfe~~~~-~~~r~~r~~l~ 159 (301)
|||||+|||+||++||||||.+.++||+|++|+ +||| ++|||||||||+||||||||++++. .+++++|++|+
T Consensus 81 LlrEk~~WE~rI~elGG~~y~k~~~Kmld~eg~--ev~~----~rGyrYFGaAkdLPgVrElFEk~~~~~~~rk~rael~ 154 (268)
T KOG3068|consen 81 LLREKHHWEVRIRELGGPNYRKYKAKMLDDEGR--EVPN----IRGYRYFGAAKDLPGVRELFEKSPEQPPPRKTRAELM 154 (268)
T ss_pred HHHHHHHHHHHHHHhcCcchhhhhhhhhhhhcc--cCCC----CCcchhhhhhccCccHHHHHhcCccCCCccchHHHHH
Confidence 999999999999999999999999999999998 9997 9999999999999999999999987 78999999999
Q ss_pred ccCCCCCccccCCCccchhhccchhHHHHHHHHHHHHHHHHHHHHHhhhhhccCccccccchhhhhhhccchhHHHHHHH
Q 022215 160 KRIDASYYGYRDDEDGVLERVEGPAEREMRAKAVQEWRRLDEIKKEAMKTVKSGEEASVMGQVNEILKEGEEDVVLEERM 239 (301)
Q Consensus 160 k~id~~YYG~~Deedg~L~~~E~~~E~~~~~~~v~~we~~~~~~~~~~~~~~~g~~~~~g~~~~~~~~~e~~~~~~~~~~ 239 (301)
++||+.||||.|++||+|+++|+..|..+++..|++|.-.+..+. |... ...++.+++.-++ +.+|.-..
T Consensus 155 k~iDa~yfgY~ddedg~L~~lE~~~E~~~~~~~v~ew~~~k~ar~--------~~~~-~deee~~~~~l~~-~~~~~~E~ 224 (268)
T KOG3068|consen 155 KRIDAEYFGYLDDEDGVLEPLEAKIESKNRERIVEEWRIEKQARK--------GPVE-EDEEEEEIYPLEE-DEEDVIEE 224 (268)
T ss_pred HhhhHHHcccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHhc--------CCcc-chhhhhhhhhccc-chhhHHHH
Confidence 999999999999999999999999999999999999983333221 1110 1011112222111 11111111
Q ss_pred HHHHHHHHhhhhhhcccccCCCHHHHHHHHHHHHHHHHHHHhhc
Q 022215 240 REMEIERKEKEREFVVHVPLPDDKEIEKMVIERKKMELLKKYAT 283 (301)
Q Consensus 240 ~~~~~~~~~~~~~f~~~v~vPt~~eIe~~LlerkK~eLL~ky~s 283 (301)
..+...++++.+.|++|||||||+|||+|||+|||++||+||+|
T Consensus 225 ~~~~~~~ed~~~~f~~hV~vPtqqdiE~~LlerrK~eLl~kya~ 268 (268)
T KOG3068|consen 225 QESEVIGEDGRPKFIAHVPVPTQQDIEEMLLERRKMELLSKYAS 268 (268)
T ss_pred HHhhhccccccccceeeccCCCHHHHHHHHHHHHHHHHHHHhcC
Confidence 22344567788899999999999999999999999999999986
No 2
>PF06246 Isy1: Isy1-like splicing family; InterPro: IPR009360 Isy1 protein is important in the optimisation of splicing [].; PDB: 1X4T_A.
Probab=100.00 E-value=1e-88 Score=629.84 Aligned_cols=249 Identities=56% Similarity=0.918 Sum_probs=64.5
Q ss_pred CCCcHHhHHHHHHHHHHHHHHhhcCCCC--CCCCCCCCCCChHHHHHHHHHHHHHHHHhHHHHhhcCCCcchhhhchHHH
Q 022215 1 MARNEEKAQSMLNRYIALQAEEKKKPKE--RRPYLASECRDLSEADKWRQQIMREIGRKVAEIQNEGLGEHRLRDLNDEI 78 (301)
Q Consensus 1 MARN~EKA~smL~R~~~~k~~e~~~~~~--rRP~~~s~v~~l~~aekWR~~Ii~EIs~kv~~Iqd~~L~E~~IRDLNDeI 78 (301)
||||+||||||||||+++|+++.++... +||++|++|+||++|++||++||+|||+||++||||+||||+||||||+|
T Consensus 1 MARN~EKA~s~L~R~~~~k~~e~~~~~~~~~RP~~~s~v~~l~~ae~WR~~ii~EIs~kv~~Iqd~~L~E~~IRdLNDeI 80 (255)
T PF06246_consen 1 MARNEEKAQSMLNRWQEQKAEEEGGYKDGSRRPKNVSEVKSLPEAEKWRRQIIKEISRKVTRIQDPSLGEFQIRDLNDEI 80 (255)
T ss_dssp -----------------------SS--------S-TTT---HHHHHHHHHHHHHHHHHHHHHHHH--S-HHHHHHHHHHH
T ss_pred CCccHHHHHHHHHHHHHHHHHhhCCcccccCCCCChhhcCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Confidence 9999999999999999999999986543 99999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhchHHHHHHhcCCCCccccccccccCCCcccCCCCCCCCCCceeeeccccCchhhhhhcCCch----hhhhcc
Q 022215 79 NKLIREKGHWERRIFELGGPNYTKHFAKMTDLEGNIVDVPNPSGRGPGYRYFGAAKKLPGVRELFEKPPE----LRKRRT 154 (301)
Q Consensus 79 NkL~rEK~~WE~rI~eLGGpdY~~~~~k~~d~~G~~~evpg~~g~~~GYrYFGrAKeLPgVkELfe~~~~----~~~r~~ 154 (301)
|+||+||+|||+||++||||||.+.+++|+|+.|+ +||| ++|||||||||+||||||||++++. ..++++
T Consensus 81 NkL~rEK~~WE~rI~~LGG~dy~~~~~~~~d~~G~--~~~~----~~GyrYFGrAkeLPgVkeL~e~~~~~~~~~~~~~~ 154 (255)
T PF06246_consen 81 NKLIREKRHWERRIKELGGPDYRRSGPKMLDSEGR--EVPG----GRGYRYFGRAKELPGVKELFEKEKKERKEEKPKKT 154 (255)
T ss_dssp HHHHHHHHHHHHHHHHHTS--STTT-------------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHhCCCCccccccccccccCc--ccCC----CCCceEeehhccCccHHHHHhccccccccccchhh
Confidence 99999999999999999999999999999999999 8998 8999999999999999999999887 678899
Q ss_pred hHHHhccCCCCCccccCCCccchhhccchhHHHHHHHHHHHHHHHHHHHHHhhhhhccCccccccchhhhhhhccchhHH
Q 022215 155 RYDIYKRIDASYYGYRDDEDGVLERVEGPAEREMRAKAVQEWRRLDEIKKEAMKTVKSGEEASVMGQVNEILKEGEEDVV 234 (301)
Q Consensus 155 r~~l~k~id~~YYG~~Deedg~L~~~E~~~E~~~~~~~v~~we~~~~~~~~~~~~~~~g~~~~~g~~~~~~~~~e~~~~~ 234 (301)
+.++++.||++||||+|++||.|+++|+++|+++...++.+|........... ..+.+.++.
T Consensus 155 ~~~~~k~i~~~YYG~~deed~~L~~~E~~~e~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~-------- 216 (255)
T PF06246_consen 155 RAELYKDIDADYYGYRDEEDGELLEYEAEAEKELREEAVEEWKEEEDEDEEKE----------EEEEEENIY-------- 216 (255)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred HHHHhhcCCccccCCCCCcchhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhc----------ccccchhhc--------
Confidence 99999999999999999999999999999999999999999987554321100 000000000
Q ss_pred HHHHHHHHHHHHHhhhhhhcccccCCCHHHHHHHHHHHHHHHHHHHh
Q 022215 235 LEERMREMEIERKEKEREFVVHVPLPDDKEIEKMVIERKKMELLKKY 281 (301)
Q Consensus 235 ~~~~~~~~~~~~~~~~~~f~~~v~vPt~~eIe~~LlerkK~eLL~ky 281 (301)
..........|++||+|||+++|++|||+|||++||+||
T Consensus 217 --------~~~~~~~~~~~~~~~~vPt~eeve~~ll~rrK~~Ll~ky 255 (255)
T PF06246_consen 217 --------KPLDEEAEDEFVAHVPVPTQEEVEKWLLERRKQELLEKY 255 (255)
T ss_dssp -----------------------------------------------
T ss_pred --------cccccccccccccCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence 000111223799999999999999999999999999998
No 3
>PF10453 NUFIP1: Nuclear fragile X mental retardation-interacting protein 1 (NUFIP1); InterPro: IPR019496 Nuclear fragile X mental retardation-interacting protein 1 (Nufip1) has been implicated in the assembly of the large subunit of the ribosome [] and in telomere maintenance []. It is known to bind RNA [] and is phosphorylated upon DNA damage []. This entry represents a conserved domain found within Nufip1. Some proteins containing this region also contain a CCCH zinc finger.
Probab=56.06 E-value=10 Score=28.45 Aligned_cols=21 Identities=33% Similarity=0.458 Sum_probs=18.0
Q ss_pred ccccCCCHHHHHHHHHHHHHH
Q 022215 255 VHVPLPDDKEIEKMVIERKKM 275 (301)
Q Consensus 255 ~~v~vPt~~eIe~~LlerkK~ 275 (301)
..+.|-|.+||++|+-+|||+
T Consensus 13 ~~~~L~t~eeI~~W~eERrk~ 33 (56)
T PF10453_consen 13 TSIKLQTPEEIAKWIEERRKN 33 (56)
T ss_pred ceeecCCHHHHHHHHHHHHHc
Confidence 445678999999999999985
No 4
>cd00319 Ribosomal_S12_like Ribosomal protein S12-like family; composed of prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins. S12 and S23 are located at the interface of the large and small ribosomal subunits, adjacent to the decoding center. They play an important role in translocation during the peptide elongation step of protein synthesis. They are also involved in important RNA and protein interactions. Ribosomal protein S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. S23 interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes translocation. Mutations in S12 and S23 have been found to affect translational accuracy. Antibiotics such as streptomycin may also bind S12/S23 and cause the ribosome to misread the genetic code.
Probab=45.62 E-value=7.7 Score=32.15 Aligned_cols=11 Identities=64% Similarity=1.011 Sum_probs=10.2
Q ss_pred eccccCchhhh
Q 022215 131 GAAKKLPGVRE 141 (301)
Q Consensus 131 GrAKeLPgVkE 141 (301)
|+++||||||-
T Consensus 70 Gr~~DlPGVry 80 (95)
T cd00319 70 GRVKDLPGVRY 80 (95)
T ss_pred CCcCCCCCcEE
Confidence 99999999985
No 5
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=29.73 E-value=33 Score=32.80 Aligned_cols=131 Identities=21% Similarity=0.339 Sum_probs=80.1
Q ss_pred hHHHHHHHHHHHHHH-hhc-CCCCCCCCCCCCCCChHHHHHHHH--HHHHHHHHhHHHHhhcCCCcchhhhchHH--HHH
Q 022215 7 KAQSMLNRYIALQAE-EKK-KPKERRPYLASECRDLSEADKWRQ--QIMREIGRKVAEIQNEGLGEHRLRDLNDE--INK 80 (301)
Q Consensus 7 KA~smL~R~~~~k~~-e~~-~~~~rRP~~~s~v~~l~~aekWR~--~Ii~EIs~kv~~Iqd~~L~E~~IRDLNDe--INk 80 (301)
-|+|..|||..+=.+ +.+ .+...+| ..|..|.+|=.=.+ +-+..+..+-+.-| -++.+-|-++.+| |-.
T Consensus 92 AansI~~Rfvsl~~g~~~~~~pe~i~~---~~~~~lrkcG~S~rK~~yLh~lA~~~~ng~--I~s~~~i~~mseEeL~~~ 166 (254)
T KOG1918|consen 92 AANSIYNRFVSLCGGAEKFPTPEFIDP---LDCEELRKCGFSKRKASYLHSLAEAYTNGY--IPSKSGIEKMSEEELIER 166 (254)
T ss_pred HHHHHHHHHHHHhCCCcCCCCchhcCc---CCHHHHHHhCcchhhHHHHHHHHHHHhcCC--CCchHHHhhcCHHHHHHH
Confidence 478999999987665 222 1334555 45777777753333 33555555554444 3455666665554 344
Q ss_pred HHHHhh--chHHHH---HHhcCCCCccccccccccCCCcccCCCCCCCCCCceeeeccccCchhhhhhcCCchhhhhcch
Q 022215 81 LIREKG--HWERRI---FELGGPNYTKHFAKMTDLEGNIVDVPNPSGRGPGYRYFGAAKKLPGVRELFEKPPELRKRRTR 155 (301)
Q Consensus 81 L~rEK~--~WE~rI---~eLGGpdY~~~~~k~~d~~G~~~evpg~~g~~~GYrYFGrAKeLPgVkELfe~~~~~~~r~~r 155 (301)
|-.-|+ .|-.+. --|+-||-.. ++++|--+||+||=.-+.||+-.++..--+.-+|-|+-
T Consensus 167 LT~VKGIg~Wtv~MflIfsL~R~DVmp---------------~dDlgir~g~k~l~gl~~~p~~~evekl~e~~kpyRtv 231 (254)
T KOG1918|consen 167 LTNVKGIGRWTVEMFLIFSLHRPDVMP---------------ADDLGIRNGVKKLLGLKPLPLPKEVEKLCEKCKPYRTV 231 (254)
T ss_pred HHhccCccceeeeeeeeeccCCCcccC---------------chhhhHHHHHHHHhCCCCCCchHHHHHHhhhccchHHH
Confidence 444444 787664 3666666442 22333468999999999999999986655555565555
Q ss_pred HH
Q 022215 156 YD 157 (301)
Q Consensus 156 ~~ 157 (301)
+-
T Consensus 232 aa 233 (254)
T KOG1918|consen 232 AA 233 (254)
T ss_pred HH
Confidence 44
No 6
>KOG1513 consensus Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription; Signal transduction mechanisms]
Probab=25.95 E-value=1.1e+02 Score=34.58 Aligned_cols=69 Identities=30% Similarity=0.412 Sum_probs=44.7
Q ss_pred ChHHHHHHHHHHHHHHHHhHHHHhhcCCCcchhhhchHHHHHHHHHhhchHHHHHHhcCCCCccccccccccCCCcccCC
Q 022215 39 DLSEADKWRQQIMREIGRKVAEIQNEGLGEHRLRDLNDEINKLIREKGHWERRIFELGGPNYTKHFAKMTDLEGNIVDVP 118 (301)
Q Consensus 39 ~l~~aekWR~~Ii~EIs~kv~~Iqd~~L~E~~IRDLNDeINkL~rEK~~WE~rI~eLGGpdY~~~~~k~~d~~G~~~evp 118 (301)
++.++|+-+. +-.|+-.||.++- +.|.-..+..| |-+||||+|-. -|+-.-|++|.-+
T Consensus 769 ~e~~~er~~~-mkeeLL~kverLg-~~LP~NTLDqL-----------------IdelGGp~~VA---EMTGRrGrvV~te 826 (1300)
T KOG1513|consen 769 DEEEAERVER-MKEELLDKVERLG-RELPPNTLDQL-----------------IDELGGPQRVA---EMTGRRGRVVSTE 826 (1300)
T ss_pred cHHHHHHHHH-HHHHHHHHHHHhc-ccCCcchHHHH-----------------HHHhCCchhHH---HhhccCceeEecC
Confidence 4456666655 5556667777765 66666555433 66899999864 4555567765555
Q ss_pred CCCCCCCCceeeeccc
Q 022215 119 NPSGRGPGYRYFGAAK 134 (301)
Q Consensus 119 g~~g~~~GYrYFGrAK 134 (301)
..+|.|=-||-
T Consensus 827 -----~g~v~ye~R~e 837 (1300)
T KOG1513|consen 827 -----DGTVAYESRAE 837 (1300)
T ss_pred -----CCceeeecccc
Confidence 34899988864
No 7
>PF10296 DUF2404: Putative integral membrane protein conserved region (DUF2404); InterPro: IPR019411 This is entry represents a domain of unknown function found in mitochondrial distribution and morphology proteins Mdm12 and Mdm34, and in maintenance of mitochondrial morphology protein Mmm1. These proteins are components of the ERMES/MDM complex, which serves as a molecular tether to connect the endoplasmic reticulum and mitochondria [].
Probab=25.80 E-value=32 Score=27.15 Aligned_cols=36 Identities=17% Similarity=0.433 Sum_probs=28.9
Q ss_pred hHHHHHHHHHHHHHHHHhHHHHhhcCC-Ccchhhhch
Q 022215 40 LSEADKWRQQIMREIGRKVAEIQNEGL-GEHRLRDLN 75 (301)
Q Consensus 40 l~~aekWR~~Ii~EIs~kv~~Iqd~~L-~E~~IRDLN 75 (301)
+.....|+..|.+-|.+|+..|.-|+. ++..|++++
T Consensus 11 ~~~t~~~~~~i~~~L~~kL~~i~~P~fl~~i~v~~~~ 47 (91)
T PF10296_consen 11 FRRTEAFRDKIKEKLQKKLNKIKLPSFLDEISVTELD 47 (91)
T ss_pred HhcCHHHHHHHHHHHHHHHccccCCCccCcEEEEEEE
Confidence 345578999999999999999998775 778888775
No 8
>CHL00051 rps12 ribosomal protein S12
Probab=25.48 E-value=26 Score=30.39 Aligned_cols=13 Identities=54% Similarity=0.833 Sum_probs=11.1
Q ss_pred eccccCchhhhhh
Q 022215 131 GAAKKLPGVRELF 143 (301)
Q Consensus 131 GrAKeLPgVkELf 143 (301)
|+.+||||||--+
T Consensus 85 Grv~DlPGVrykv 97 (123)
T CHL00051 85 GRVKDLPGVRYHI 97 (123)
T ss_pred CccCCCCCeeEEE
Confidence 8999999998643
No 9
>COG3890 ERG8 Phosphomevalonate kinase [Lipid metabolism]
Probab=22.67 E-value=1.6e+02 Score=29.36 Aligned_cols=91 Identities=29% Similarity=0.296 Sum_probs=62.7
Q ss_pred hHHHHHHHHHHHHHHHHhHHHHhhcCCCcchhhhch------HHHHHHHHHhhchHHHHHHhcCCCCcccc-----cccc
Q 022215 40 LSEADKWRQQIMREIGRKVAEIQNEGLGEHRLRDLN------DEINKLIREKGHWERRIFELGGPNYTKHF-----AKMT 108 (301)
Q Consensus 40 l~~aekWR~~Ii~EIs~kv~~Iqd~~L~E~~IRDLN------DeINkL~rEK~~WE~rI~eLGGpdY~~~~-----~k~~ 108 (301)
+..-.+||..++=|+.+.+-..+ =|-|| ||.|.-++--++-=+||.++|+.|-.... ++..
T Consensus 210 V~kv~~w~ns~~peelkc~de~n--------srvl~l~~~sLdE~~s~~~~irrslrritee~~adiep~kqt~~Ld~i~ 281 (337)
T COG3890 210 VCKVNKWRNSILPEELKCNDEMN--------SRVLNLIKLSLDESNSKSKAIRRSLRRITEEGLADIEPIKQTAALDSIF 281 (337)
T ss_pred HHHHHHHhhcCChHHHHhHHHHH--------HHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHhccccccchhhhhhhhHH
Confidence 56778899999777777554444 34444 56776666667788899999998866533 3344
Q ss_pred ccCCCc-ccCCCCCCCCCCceeeeccccCchhhh
Q 022215 109 DLEGNI-VDVPNPSGRGPGYRYFGAAKKLPGVRE 141 (301)
Q Consensus 109 d~~G~~-~evpg~~g~~~GYrYFGrAKeLPgVkE 141 (301)
+..|.+ +-+|| .|.|=--|==++.+-+++|
T Consensus 282 ~l~gvl~~lipg---aGggdaif~l~~~~~e~re 312 (337)
T COG3890 282 DLLGVLCDLIPG---AGGGDAIFLLYRPNIEARE 312 (337)
T ss_pred hccCceEeeccc---CCCCceEEEEecccHHHHH
Confidence 556664 23576 4445578888899999888
No 10
>cd03368 Ribosomal_S12 S12-like family, 30S ribosomal protein S12 subfamily; S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria, where it plays an important role in both tRNA and ribosomal subunit interactions. S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. Antibiotics such as streptomycin bind S12 and cause the ribosome to misread the genetic code.
Probab=22.39 E-value=31 Score=29.24 Aligned_cols=11 Identities=64% Similarity=1.011 Sum_probs=10.2
Q ss_pred eccccCchhhh
Q 022215 131 GAAKKLPGVRE 141 (301)
Q Consensus 131 GrAKeLPgVkE 141 (301)
|+.+||||||-
T Consensus 83 Grv~DlPGVky 93 (108)
T cd03368 83 GRVKDLPGVRY 93 (108)
T ss_pred CccCCCCCeEE
Confidence 99999999985
No 11
>PRK05163 rpsL 30S ribosomal protein S12; Validated
Probab=22.37 E-value=32 Score=29.82 Aligned_cols=13 Identities=54% Similarity=0.833 Sum_probs=11.2
Q ss_pred eccccCchhhhhh
Q 022215 131 GAAKKLPGVRELF 143 (301)
Q Consensus 131 GrAKeLPgVkELf 143 (301)
|+.+||||||--+
T Consensus 85 Grv~DlPGVrykv 97 (124)
T PRK05163 85 GRVKDLPGVRYHI 97 (124)
T ss_pred CccCCCCCcEEEE
Confidence 8999999998644
No 12
>TIGR00981 rpsL_bact ribosomal protein S12, bacterial/organelle. This model recognizes ribosomal protein S12 of Bacteria, mitochondria, and chloroplasts. The homologous ribosomal proteins of Archaea and Eukarya, termed S23 in Eukarya and S12 or S23 in Archaea, score below the trusted cutoff.
Probab=22.18 E-value=32 Score=29.83 Aligned_cols=13 Identities=54% Similarity=0.833 Sum_probs=11.1
Q ss_pred eccccCchhhhhh
Q 022215 131 GAAKKLPGVRELF 143 (301)
Q Consensus 131 GrAKeLPgVkELf 143 (301)
|+.+||||||--+
T Consensus 85 Grv~DlPGVkykv 97 (124)
T TIGR00981 85 GRVKDLPGVRYHI 97 (124)
T ss_pred CccCCCCCeEEEE
Confidence 8999999998643
No 13
>TIGR03504 FimV_Cterm FimV C-terminal domain. This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.
Probab=21.37 E-value=67 Score=22.73 Aligned_cols=23 Identities=35% Similarity=0.434 Sum_probs=15.6
Q ss_pred HHHHHhhcHHHHHHHHHHHHhhc
Q 022215 276 ELLKKYATEEFVEEQNEAKAMLN 298 (301)
Q Consensus 276 eLL~ky~s~~l~~~~~eak~~l~ 298 (301)
+||+...+..--.|+++|++||+
T Consensus 20 ~lL~evl~~~~~~q~~eA~~LL~ 42 (44)
T TIGR03504 20 ELLEEVIEEGDEAQRQEARALLA 42 (44)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHh
Confidence 45555555555678888888875
No 14
>PF00164 Ribosom_S12_S23: Ribosomal protein S12/S23; InterPro: IPR006032 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 S12 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S12 is known to be involved in the translation initiation step. It is a very basic protein of 120 to 150 amino-acid residues. S12 belongs to a family of ribosomal proteins which are grouped on the basis of sequence similarities. This protein is known typically as S12 in bacteria, S23 in eukaryotes and as either S12 or S23 in the Archaea []. Bacterial S12 molecules contain a conserved aspartic acid residue which undergoes a novel post-translational modification, beta-methylthiolation, to form the corresponding 3-methylthioaspartic acid.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZKQ_l 3BBN_L 3PYU_L 3D5A_L 3MS0_L 3MR8_L 3F1G_L 2OW8_m 3PYS_L 2QNH_m ....
Probab=20.98 E-value=40 Score=29.14 Aligned_cols=17 Identities=29% Similarity=0.280 Sum_probs=13.1
Q ss_pred eeeeccccCchhhhhhc
Q 022215 128 RYFGAAKKLPGVRELFE 144 (301)
Q Consensus 128 rYFGrAKeLPgVkELfe 144 (301)
-..|+.+|||||+-=+-
T Consensus 81 VrGgrv~DlPGVkykvV 97 (122)
T PF00164_consen 81 VRGGRVGDLPGVKYKVV 97 (122)
T ss_dssp EEEESBTTSTTECEEBE
T ss_pred EeccccCCCCceEEEEE
Confidence 35688999999986443
Done!