Query psy8505
Match_columns 118
No_of_seqs 74 out of 76
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 20:39:37 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8505.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8505hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4309|consensus 100.0 1.5E-35 3.2E-40 231.9 9.3 103 3-117 45-148 (217)
2 PF08612 Med20: TATA-binding r 100.0 3.3E-30 7.2E-35 201.4 11.0 112 3-115 46-164 (225)
3 KOG1383|consensus 94.5 0.011 2.5E-07 52.4 0.2 63 52-117 166-230 (491)
4 CHL00142 rps17 ribosomal prote 63.2 16 0.00035 25.3 4.2 62 52-116 17-79 (84)
5 PF14302 DUF4377: Domain of un 57.5 12 0.00027 25.2 2.8 39 73-114 32-77 (80)
6 PF04265 TPK_B1_binding: Thiam 51.7 6.9 0.00015 25.1 0.7 28 79-106 25-53 (68)
7 TIGR01378 thi_PPkinase thiamin 37.9 46 0.00099 25.6 3.5 39 80-118 159-198 (203)
8 cd07995 TPK Thiamine pyrophosp 35.6 42 0.00091 25.7 3.0 30 79-108 161-191 (208)
9 cd04713 BAH_plant_3 BAH, or Br 35.4 79 0.0017 23.4 4.3 35 79-114 12-46 (146)
10 PF00924 MS_channel: Mechanose 32.2 23 0.00051 26.1 1.0 22 87-115 60-81 (206)
11 PF00181 Ribosomal_L2: Ribosom 31.3 50 0.0011 22.0 2.4 14 105-118 32-45 (77)
12 COG3510 CmcI Cephalosporin hyd 29.3 71 0.0015 26.3 3.4 78 10-100 90-182 (237)
13 PF02014 Reeler: Reeler domain 27.7 86 0.0019 22.1 3.3 35 81-116 23-58 (132)
14 PLN02714 thiamin pyrophosphoki 26.7 79 0.0017 25.0 3.2 37 80-116 183-220 (229)
15 KOG3153|consensus 25.3 1.1E+02 0.0024 25.5 3.9 37 79-115 201-238 (250)
16 PRK00199 ihfB integration host 24.7 1.1E+02 0.0024 20.5 3.3 48 56-113 24-72 (94)
17 PF07935 SSV1_ORF_D-335: ORF D 24.5 51 0.0011 22.7 1.5 11 87-97 2-12 (72)
18 cd08544 Reeler Reeler, the N-t 23.6 1.4E+02 0.003 21.0 3.8 36 80-116 22-58 (135)
19 PF12961 DUF3850: Domain of Un 22.3 2.3E+02 0.0051 19.2 4.4 47 62-116 10-57 (72)
20 PF00366 Ribosomal_S17: Riboso 22.0 82 0.0018 20.7 2.1 59 52-113 10-69 (69)
21 PF13856 Gifsy-2: ATP-binding 21.4 47 0.001 22.6 0.9 31 59-89 2-32 (95)
22 cd04715 BAH_Orc1p_like BAH, or 21.3 81 0.0018 24.0 2.3 33 80-115 22-55 (159)
23 PF08940 DUF1918: Domain of un 20.3 31 0.00068 22.7 -0.2 25 89-113 4-28 (58)
No 1
>KOG4309|consensus
Probab=100.00 E-value=1.5e-35 Score=231.88 Aligned_cols=103 Identities=39% Similarity=0.656 Sum_probs=97.1
Q ss_pred eEeecCccccccCCC-cEEEEEecCCCCCeEEEEEcCCCCCCCCCCCCCceeeeeeecchHHHHHHhcccceeeccceEE
Q psy8505 3 TYHAGTGRYAHLGSQ-KTVHVLHNSEQPASVFSILESGVPGGPGGPSGAVKNIPVVADSLFDLLMMKMTPVYTSKKQTKV 81 (118)
Q Consensus 3 ty~~~~~~~~~~g~~-r~~~~l~~se~P~s~F~i~~~~~~~~~~~~~~~~k~~~l~aD~~fd~im~kL~s~y~~r~~~ki 81 (118)
|||++++ .+-|+| |.+|||||||||+|+|+|++|++ +|+++++||+.||+||.||++++++++++||
T Consensus 45 tF~~~~~--~~~g~~g~~~~VmHnSeyP~STFSI~~ngT----------fKks~~VaD~~FDLlm~Kl~~~f~s~ka~KI 112 (217)
T KOG4309|consen 45 TFHTAAS--TLGGQTGKLMYVMHNSEYPLSTFSIFENGT----------FKKSCLVADTNFDLLMVKLKGFFQSAKASKI 112 (217)
T ss_pred ccCCCCC--CCCCCcCceEEEEecCCCCcceeEEecCCC----------cceeEEEecCCcceeehhhccceeeccccce
Confidence 6788776 244678 99999999999999999999996 7899999999999999999999999999999
Q ss_pred EEccceeEeCCeEEEEeeeEecCcccEEEEEEEEeC
Q psy8505 82 ESKGPRFELGDFCVKLGSVSISQNFKAVLVEVRTSK 117 (118)
Q Consensus 82 e~~G~~YelGDF~VrvG~Vt~~~~~rGilvEVEY~~ 117 (118)
|++|.||++|||.||||+|+||+.+|||+|||||.+
T Consensus 113 E~rG~ry~Y~Df~IkvGtvTmg~tvKGi~vEIEY~p 148 (217)
T KOG4309|consen 113 ETRGTRYQYCDFLIKVGTVTMGPTVKGISVEIEYGP 148 (217)
T ss_pred eeccceeeecceEEEEcceEeccccceEEEEEeeCC
Confidence 999999999999999999999999999999999975
No 2
>PF08612 Med20: TATA-binding related factor (TRF) of subunit 20 of Mediator complex; InterPro: IPR013921 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Proteins in this entry are subunit Med20 of the Mediator complex, and is found in the non-essential part of the head []. and related to the TATA-binding protein (TBP). TBP is a highly conserved RNA polymerase II general transcription factor that binds to the core promoter and initiates assembly of the pre-initiation complex. Human TRF has been shown to associate with an RNA polymerase II-SRB complex []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 2HZS_C 3RJ1_M 2HZM_G.
Probab=99.97 E-value=3.3e-30 Score=201.38 Aligned_cols=112 Identities=34% Similarity=0.561 Sum_probs=85.9
Q ss_pred eEeecCcccc---ccCCCcEEEEEecCCCCCeEEEEEcCCCCCCCCCCC---CCceee-eeeecchHHHHHHhcccceee
Q psy8505 3 TYHAGTGRYA---HLGSQKTVHVLHNSEQPASVFSILESGVPGGPGGPS---GAVKNI-PVVADSLFDLLMMKMTPVYTS 75 (118)
Q Consensus 3 ty~~~~~~~~---~~g~~r~~~~l~~se~P~s~F~i~~~~~~~~~~~~~---~~~k~~-~l~aD~~fd~im~kL~s~y~~ 75 (118)
+|+..+.... ...+||+||+||+||+|++||+|+++++.+.+.++. +-++.+ ++++|+.|++||.||+++|++
T Consensus 46 ~yr~~~~~~p~~~~~~~~r~~~~L~~S~~p~~~f~i~~~~~~~~~~~~~~~~~~~~~~~~~~~D~~~~~i~~KL~~~w~~ 125 (225)
T PF08612_consen 46 TYRDTPSSLPASQPPSQPRYMYVLSLSEYPNSTFIIINNGPAKTTTNSQTNSHLMNGCPTLVADSFFDLIMSKLQSLWTQ 125 (225)
T ss_dssp EEEE-SSS------SSS-SEEEEEEEESSSEEEEEEETTEEEEEES-GGGHHHHHTTSS-S-B--HHHHHHHHSTTTEEE
T ss_pred EecCCCCCCCcccccccccEEEEEecccCCCcEEEEEcCCCcccccccCCccceeccccccccChHHHHHHHHHHhhhhh
Confidence 6777776332 124689999999999999999999998522222210 001222 699999999999999999999
Q ss_pred ccceEEEEccceeEeCCeEEEEeeeEecCcccEEEEEEEE
Q psy8505 76 KKQTKVESKGPRFELGDFCVKLGSVSISQNFKAVLVEVRT 115 (118)
Q Consensus 76 r~~~kie~~G~~YelGDF~VrvG~Vt~~~~~rGilvEVEY 115 (118)
|++.|+|.+|. ||+|||+||+|+|++++++|||||||||
T Consensus 126 Rq~~kie~~~~-YelgDf~VRvg~v~~~~~~rGilvEVEy 164 (225)
T PF08612_consen 126 RQTIKIEGGGT-YELGDFTVRVGNVFQGQSFRGILVEVEY 164 (225)
T ss_dssp EEEEEEESEEE-EEETTEEEEEEEEEETTEEEEEEEEEEE
T ss_pred cEEEEEeeeeE-EEECCEEEEEEEEEECCCCcEEEEEEEE
Confidence 99999999999 9999999999999999999999999999
No 3
>KOG1383|consensus
Probab=94.48 E-value=0.011 Score=52.38 Aligned_cols=63 Identities=17% Similarity=0.107 Sum_probs=56.1
Q ss_pred eeeeeeecchHHHHHHhcccceeeccceEEEEccceeEeCCeEEEEeee--EecCcccEEEEEEEEeC
Q psy8505 52 KNIPVVADSLFDLLMMKMTPVYTSKKQTKVESKGPRFELGDFCVKLGSV--SISQNFKAVLVEVRTSK 117 (118)
Q Consensus 52 k~~~l~aD~~fd~im~kL~s~y~~r~~~kie~~G~~YelGDF~VrvG~V--t~~~~~rGilvEVEY~~ 117 (118)
|.+....|..-++++++++. |.+... ++.++..|+.|||.+++|.+ ...++.+|++++++|.+
T Consensus 166 k~I~~p~iv~~~~v~~a~eK-~a~yf~--v~l~~V~~~~~~~~~D~~k~~~~i~eNti~lv~~~~~~p 230 (491)
T KOG1383|consen 166 KGIDKPNIVTPQNVHAAFEK-AARYFE--VELREVPLDEGDYRVDPGKVVRMIDENTIMLVGSLPNFP 230 (491)
T ss_pred cCCCCccccchHHHHHHHHH-HHhhEE--EEEEeeeccccceEecHHHHHHHhccceEEEEEEcCCCC
Confidence 46778888889999999998 777775 99999999999999999999 77799999999999875
No 4
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=63.16 E-value=16 Score=25.35 Aligned_cols=62 Identities=19% Similarity=0.261 Sum_probs=35.7
Q ss_pred eeeeeeecchHHHHHHhcccceeeccceEEEEccceeEeCCeEEEEeee-EecCcccEEEEEEEEe
Q psy8505 52 KNIPVVADSLFDLLMMKMTPVYTSKKQTKVESKGPRFELGDFCVKLGSV-SISQNFKAVLVEVRTS 116 (118)
Q Consensus 52 k~~~l~aD~~fd~im~kL~s~y~~r~~~kie~~G~~YelGDF~VrvG~V-t~~~~~rGilvEVEY~ 116 (118)
|++.+..+..+-. .+.+-..+..+.-.+--+...-++|| .|+|+.. -.+-+.+++++||.-.
T Consensus 17 KTivV~v~r~~~h--~kY~K~~~r~kk~~aHDe~n~~~~GD-~V~I~e~RPlSKtK~~~v~~i~~~ 79 (84)
T CHL00142 17 KTIVVAVENRYKH--PIYGKIITKTKKYLVHDEENECNIGD-QVLIEETRPLSKTKRWILKEILSK 79 (84)
T ss_pred ceEEEEEEEEEEc--CcccEEEEeeEEEEEeCCCCCCCCCC-EEEEEEcCCCCCcEEEEEEEEEEe
Confidence 7777777776533 22223122222111222334466788 5677766 5567999999999644
No 5
>PF14302 DUF4377: Domain of unknown function (DUF4377)
Probab=57.54 E-value=12 Score=25.19 Aligned_cols=39 Identities=15% Similarity=0.393 Sum_probs=29.6
Q ss_pred eeeccceEEEEccceeEeC-CeEEEEeeeEe------cCcccEEEEEEE
Q psy8505 73 YTSKKQTKVESKGPRFELG-DFCVKLGSVSI------SQNFKAVLVEVR 114 (118)
Q Consensus 73 y~~r~~~kie~~G~~YelG-DF~VrvG~Vt~------~~~~rGilvEVE 114 (118)
|+.-. =.|+|..||-| .+.|||-.... +.+.|-+|++|-
T Consensus 32 W~~fy---~~IeGF~yE~Gy~Y~L~Vk~~~~~nppaD~ss~~Y~L~~vi 77 (80)
T PF14302_consen 32 WELFY---GSIEGFEYEPGYEYVLRVKRTPVANPPADASSYRYVLIKVI 77 (80)
T ss_pred cEECc---CcccCcCcCCCcEEEEEEEEEECCCCCCCCCceeEEEEEEE
Confidence 55433 35899999999 99999987742 358899999873
No 6
>PF04265 TPK_B1_binding: Thiamin pyrophosphokinase, vitamin B1 binding domain; InterPro: IPR007373 Thiamin pyrophosphokinase (TPK, 2.7.6.2 from EC) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus, TPK is important for the formation of a coenzyme required for central metabolic functions. The structure of thiamin pyrophosphokinase suggest that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis [].; GO: 0004788 thiamine diphosphokinase activity, 0009229 thiamine diphosphate biosynthetic process; PDB: 3LM8_B 1IG0_A 3CQ9_A 3L8M_B 3IHK_B 3MEL_B 2HH9_A 2F17_B 1IG3_B 2G9Z_A ....
Probab=51.71 E-value=6.9 Score=25.08 Aligned_cols=28 Identities=32% Similarity=0.646 Sum_probs=22.9
Q ss_pred eEEEEccceeEeCCeEEEEeee-EecCcc
Q psy8505 79 TKVESKGPRFELGDFCVKLGSV-SISQNF 106 (118)
Q Consensus 79 ~kie~~G~~YelGDF~VrvG~V-t~~~~~ 106 (118)
.++.++|.+|+|-|+.+..|.. ..+..+
T Consensus 25 ~~vt~~Glky~L~~~~l~~~~~~~~SNe~ 53 (68)
T PF04265_consen 25 VTVTIKGLKYPLDNYTLSFGSSIGISNEF 53 (68)
T ss_dssp EEEEEESBSSEEEEEEEBTTTBTEEEEEB
T ss_pred eEEEEeCCEEECccceecCCCeeEECeEE
Confidence 3499999999999999998877 555555
No 7
>TIGR01378 thi_PPkinase thiamine pyrophosphokinase. This model has been revised. Originally, it described strictly eukaryotic thiamine pyrophosphokinase. However, it is now expanded to include also homologous enzymes, apparently functionally equivalent, from species that rely on thiamine pyrophosphokinase rather than thiamine-monophosphate kinase (TIGR01379) to produce the active TPP cofactor. This includes the thiamine pyrophosphokinase from Bacillus subtilis, previously designated YloS.
Probab=37.92 E-value=46 Score=25.65 Aligned_cols=39 Identities=26% Similarity=0.440 Sum_probs=28.2
Q ss_pred EEEEccceeEeCCeEEEEee-eEecCcccEEEEEEEEeCC
Q psy8505 80 KVESKGPRFELGDFCVKLGS-VSISQNFKAVLVEVRTSKG 118 (118)
Q Consensus 80 kie~~G~~YelGDF~VrvG~-Vt~~~~~rGilvEVEY~~~ 118 (118)
.+.++|.+|.|-+..+..|. +..+..+.+=-++|+...|
T Consensus 159 ~vt~~Glky~L~~~~l~~~~~~~~SNe~~~~~~~I~~~~G 198 (203)
T TIGR01378 159 GLTTKGLKYPLNNAHLKFGGSRGISNEFIGNKATVSVESG 198 (203)
T ss_pred cEEeeCCEeecCCceeeCCCeeEECeeEECCcEEEEEcCC
Confidence 48999999999999998884 5555555554466665543
No 8
>cd07995 TPK Thiamine pyrophosphokinase. Thiamine pyrophosphokinase (TPK, EC:2.7.6.2, also spelled thiamin pyrophosphokinase) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamine) to form the coenzyme thiamine pyrophosphate (TPP). TPP is required for central metabolic functions, and thiamine deficiency is associated with potentially fatal human diseases. The structure of thiamine pyrophosphokinase suggests that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis.
Probab=35.63 E-value=42 Score=25.68 Aligned_cols=30 Identities=27% Similarity=0.470 Sum_probs=22.8
Q ss_pred eEEEEccceeEeCCeEEEEeee-EecCcccE
Q psy8505 79 TKVESKGPRFELGDFCVKLGSV-SISQNFKA 108 (118)
Q Consensus 79 ~kie~~G~~YelGDF~VrvG~V-t~~~~~rG 108 (118)
..+..+|.+|.+-|+.++.|.. ..+..+.+
T Consensus 161 ~~vt~~Glky~L~~~~l~~~~~~~~SNe~~~ 191 (208)
T cd07995 161 TGLTLKGLKYPLDNATLSFGSSLGTSNEFTG 191 (208)
T ss_pred cceEEeCCEEecCCceEeCCCeEEEeEEEeC
Confidence 3599999999999999987665 44544444
No 9
>cd04713 BAH_plant_3 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=35.43 E-value=79 Score=23.37 Aligned_cols=35 Identities=17% Similarity=0.382 Sum_probs=22.2
Q ss_pred eEEEEccceeEeCCeEEEEeeeEecCcccEEEEEEE
Q psy8505 79 TKVESKGPRFELGDFCVKLGSVSISQNFKAVLVEVR 114 (118)
Q Consensus 79 ~kie~~G~~YelGDF~VrvG~Vt~~~~~rGilvEVE 114 (118)
..++.+|..|++||+..=-..-. .+..=|+|+|+.
T Consensus 12 ~s~~~dg~~y~vgD~Vlv~~~~~-~~pyI~~I~~i~ 46 (146)
T cd04713 12 TSFEKDGNKYRLEDCVLLVPEDD-QKPYIAIIKDIY 46 (146)
T ss_pred eeEEECCEEEECCCEEEEeCCCC-CCCEEEEEEEEE
Confidence 45899999999999976332111 223345666664
No 10
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=32.18 E-value=23 Score=26.12 Aligned_cols=22 Identities=23% Similarity=0.537 Sum_probs=12.8
Q ss_pred eeEeCCeEEEEeeeEecCcccEEEEEEEE
Q psy8505 87 RFELGDFCVKLGSVSISQNFKAVLVEVRT 115 (118)
Q Consensus 87 ~YelGDF~VrvG~Vt~~~~~rGilvEVEY 115 (118)
.|++||| |+++ ..+|.+.|+..
T Consensus 60 pf~vGD~-I~i~------~~~G~V~~I~l 81 (206)
T PF00924_consen 60 PFKVGDR-IEIG------GVEGRVEEIGL 81 (206)
T ss_dssp SS-TT-E-EESS------S-EEEEEEE-S
T ss_pred CccCCCE-EEEE------EeehHHHhcCc
Confidence 5788998 7776 56677777653
No 11
>PF00181 Ribosomal_L2: Ribosomal Proteins L2, RNA binding domain; InterPro: IPR022666 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 L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1YIT_A 1Q7Y_C 1YJN_A 3CPW_A 3I56_A 1VQ9_A 1M1K_C 3CC7_A 1YIJ_A 1K9M_C ....
Probab=31.34 E-value=50 Score=21.96 Aligned_cols=14 Identities=14% Similarity=0.503 Sum_probs=12.1
Q ss_pred cccEEEEEEEEeCC
Q psy8505 105 NFKAVLVEVRTSKG 118 (118)
Q Consensus 105 ~~rGilvEVEY~~~ 118 (118)
..+|++++|||.++
T Consensus 32 ~~~g~V~~i~~DP~ 45 (77)
T PF00181_consen 32 NIKGIVIDIEYDPN 45 (77)
T ss_dssp SEEEEEEEEEEETT
T ss_pred CCcEEEEEEEecCC
Confidence 47899999999875
No 12
>COG3510 CmcI Cephalosporin hydroxylase [Defense mechanisms]
Probab=29.27 E-value=71 Score=26.34 Aligned_cols=78 Identities=14% Similarity=0.143 Sum_probs=51.0
Q ss_pred cccccCCCcEEEEEecCCCC-------CeEEEEEcCCCCCCCCCC-------CCCcee-eeeeecchHHHHHHhccccee
Q psy8505 10 RYAHLGSQKTVHVLHNSEQP-------ASVFSILESGVPGGPGGP-------SGAVKN-IPVVADSLFDLLMMKMTPVYT 74 (118)
Q Consensus 10 ~~~~~g~~r~~~~l~~se~P-------~s~F~i~~~~~~~~~~~~-------~~~~k~-~~l~aD~~fd~im~kL~s~y~ 74 (118)
.+-..|||+.+..++.+..| .+.-..+++. .+||..- +++.|- +|+-+|-..++.|.-|+- |.
T Consensus 90 ~m~s~Gq~~kvl~vdIdi~~~~p~a~e~p~i~f~egs-s~dpai~eqi~~~~~~y~kIfvilDsdHs~~hvLAel~~-~~ 167 (237)
T COG3510 90 MMISIGQPFKVLGVDIDIKPLDPAAREVPDILFIEGS-STDPAIAEQIRRLKNEYPKIFVILDSDHSMEHVLAELKL-LA 167 (237)
T ss_pred hHHhcCCCceEEEEecccCcCChhhhcCCCeEEEeCC-CCCHHHHHHHHHHhcCCCcEEEEecCCchHHHHHHHHHH-hh
Confidence 34456899999999999888 4555555554 3444322 444444 569999999999987776 44
Q ss_pred eccceEEEEccceeEeCCeEEEEeee
Q psy8505 75 SKKQTKVESKGPRFELGDFCVKLGSV 100 (118)
Q Consensus 75 ~r~~~kie~~G~~YelGDF~VrvG~V 100 (118)
+=. ..|||+|-.-++
T Consensus 168 pll-----------saG~Y~vVeDs~ 182 (237)
T COG3510 168 PLL-----------SAGDYLVVEDSN 182 (237)
T ss_pred hHh-----------hcCceEEEeccc
Confidence 433 236777655443
No 13
>PF02014 Reeler: Reeler domain Schematic picture including Reeler domain; InterPro: IPR002861 Extracellular matrix (ECM) proteins play an important role in early cortical development, specifically in the formation of neural connections and in controlling the cyto-architecture of the central nervous system. The product of the reeler gene in mouse is reelin,a large extracellular protein secreted by pioneer neurons that coordinates cell positioning during neurodevelopment []. F-spondin and mindin are a family of matrix-attached adhesion molecules that share structural similarities and overlapping domains of expression. Both F-spondin and mindin promote adhesion and outgrowth of hippocampal embryonic neurons and bind to a putative receptor(s) expressed on both hippocampal and sensory neurons []. This domain of unknown function is found at the N terminus of reelin and F-spondin.; PDB: 2ZOT_B 2ZOU_B 3COO_A.
Probab=27.68 E-value=86 Score=22.14 Aligned_cols=35 Identities=29% Similarity=0.496 Sum_probs=23.8
Q ss_pred EEEccceeEeC-CeEEEEeeeEecCcccEEEEEEEEe
Q psy8505 81 VESKGPRFELG-DFCVKLGSVSISQNFKAVLVEVRTS 116 (118)
Q Consensus 81 ie~~G~~YelG-DF~VrvG~Vt~~~~~rGilvEVEY~ 116 (118)
|.+.-..|+-| -+.|.+ +.+-+..+||.+|..+..
T Consensus 23 i~~~~~~y~pg~~~~Vtl-~~~~~~~F~GFllqAr~~ 58 (132)
T PF02014_consen 23 ISVSPSSYEPGQTYTVTL-SSSGSSSFRGFLLQARDA 58 (132)
T ss_dssp EEET-SSB-TTBEEEEEE-EETTTEEBSEEEEEEEET
T ss_pred EEeCCCeEcCCCEEEEEE-ECCCCCceeEEEEEEEeC
Confidence 44444457766 678887 556668999999998754
No 14
>PLN02714 thiamin pyrophosphokinase
Probab=26.69 E-value=79 Score=25.00 Aligned_cols=37 Identities=22% Similarity=0.337 Sum_probs=27.2
Q ss_pred EEEEccceeEeCCeEEEEeee-EecCcccEEEEEEEEe
Q psy8505 80 KVESKGPRFELGDFCVKLGSV-SISQNFKAVLVEVRTS 116 (118)
Q Consensus 80 kie~~G~~YelGDF~VrvG~V-t~~~~~rGilvEVEY~ 116 (118)
.+..+|.+|.|-|+.+.+|.. +.+..+.+=-++|+..
T Consensus 183 ~vt~~Glky~L~~~~l~~~~~~~vSNe~~~~~v~I~~~ 220 (229)
T PLN02714 183 STTTTGLQWNLDNTEMRFGGLISTSNIVKEDKVTVESD 220 (229)
T ss_pred eEEeeCceeeCCCCeeeCCCceEEeeEEcCCEEEEEeC
Confidence 499999999999999999854 4444454445666654
No 15
>KOG3153|consensus
Probab=25.28 E-value=1.1e+02 Score=25.45 Aligned_cols=37 Identities=27% Similarity=0.447 Sum_probs=27.9
Q ss_pred eEEEEccceeEeCCeEEEEeee-EecCcccEEEEEEEE
Q psy8505 79 TKVESKGPRFELGDFCVKLGSV-SISQNFKAVLVEVRT 115 (118)
Q Consensus 79 ~kie~~G~~YelGDF~VrvG~V-t~~~~~rGilvEVEY 115 (118)
+..+..|.++.+-+++.++|.. +-+..+.|=.|-||-
T Consensus 201 ~~ktT~GLkWnl~n~~~~fgglvStsN~~~~~~vtvet 238 (250)
T KOG3153|consen 201 TVKTTTGLKWNLSNRRMKFGGLVSTSNTYDGEVVTVET 238 (250)
T ss_pred eeeeecccccccccceeecceEEeecceeeccEEEEec
Confidence 3466788889998888888765 666777887777774
No 16
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=24.66 E-value=1.1e+02 Score=20.46 Aligned_cols=48 Identities=17% Similarity=0.328 Sum_probs=32.6
Q ss_pred eeecchHHHHHHhcccceeeccceEEEEccceeEeCCeEEEEeeeEecCccc-EEEEEE
Q psy8505 56 VVADSLFDLLMMKMTPVYTSKKQTKVESKGPRFELGDFCVKLGSVSISQNFK-AVLVEV 113 (118)
Q Consensus 56 l~aD~~fd~im~kL~s~y~~r~~~kie~~G~~YelGDF~VrvG~Vt~~~~~r-GilvEV 113 (118)
.+.|..++.|.+.|... .+|++.| +|-|.++.=.-.+|-+++ |-.++|
T Consensus 24 ~vv~~~~~~i~~~L~~g------~~V~l~g----fG~F~~~~r~~r~~~np~Tge~i~i 72 (94)
T PRK00199 24 NAVKEILEEMSDALARG------DRIEIRG----FGSFSLHYRPPRVGRNPKTGEKVEL 72 (94)
T ss_pred HHHHHHHHHHHHHHHcC------CeEEEcC----CEEEEEEEecCeeccCcCCCCEEEE
Confidence 56677778888777664 3466665 688888876667775655 665555
No 17
>PF07935 SSV1_ORF_D-335: ORF D-335-like protein; InterPro: IPR012922 The sequences featured in this family are similar to a probable integrase (P20214 from SWISSPROT) expressed by the SSV1 virus of the archaeon Sulfolobus shibatae. This protein may be necessary for the integration of the virus into the host genome by a process of site-specific recombination [].
Probab=24.46 E-value=51 Score=22.68 Aligned_cols=11 Identities=18% Similarity=0.622 Sum_probs=9.3
Q ss_pred eeEeCCeEEEE
Q psy8505 87 RFELGDFCVKL 97 (118)
Q Consensus 87 ~YelGDF~Vrv 97 (118)
+|.+|||+||=
T Consensus 2 ~y~~gd~~irE 12 (72)
T PF07935_consen 2 VYKFGDIIIRE 12 (72)
T ss_pred eeecCcEEEEE
Confidence 68999999983
No 18
>cd08544 Reeler Reeler, the N-terminal domain of reelin, F-spondin, and a variety of other proteins. This domain is found at the N-terminus of F-spondin, a protein attached to the extracellular matrix, which plays roles in neuronal development and vascular remodelling. The F-spondin reeler domain has been reported to bind heparin. The reeler domain is also found at the N-terminus of reelin, an extracellular glycoprotein involved in the development of the brain cortex, and in a variety of other eukaryotic proteins with different domain architectures, including the animal ferric-chelate reductase 1 or stromal cell-derived receptor 2, a member of the cytochrome B561 family, which reduces ferric iron before its transport from the endosome to the cytoplasm. Also included is the insect putative defense protein 1, which is expressed upon bacterial infection and appears to contain a single reeler domain.
Probab=23.63 E-value=1.4e+02 Score=21.02 Aligned_cols=36 Identities=22% Similarity=0.454 Sum_probs=21.8
Q ss_pred EEEEccceeEeC-CeEEEEeeeEecCcccEEEEEEEEe
Q psy8505 80 KVESKGPRFELG-DFCVKLGSVSISQNFKAVLVEVRTS 116 (118)
Q Consensus 80 kie~~G~~YelG-DF~VrvG~Vt~~~~~rGilvEVEY~ 116 (118)
.|.+.+..|.-| .+.|-+..-.. ..+||.+|+++..
T Consensus 22 ~i~~~~~~y~pG~~~~Vtl~~~~~-~~F~GF~lqAr~~ 58 (135)
T cd08544 22 SITISGNSYVPGETYTVTLSGSSP-SPFRGFLLQARDA 58 (135)
T ss_pred EEEeCCCEECCCCEEEEEEECCCC-CceeEEEEEEEcC
Confidence 366667777777 44443322111 4799999988753
No 19
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=22.30 E-value=2.3e+02 Score=19.20 Aligned_cols=47 Identities=13% Similarity=0.186 Sum_probs=27.5
Q ss_pred HHHHHHhcccceeeccceEEEEccceeEeCCeEEEEeeeEec-CcccEEEEEEEEe
Q psy8505 62 FDLLMMKMTPVYTSKKQTKVESKGPRFELGDFCVKLGSVSIS-QNFKAVLVEVRTS 116 (118)
Q Consensus 62 fd~im~kL~s~y~~r~~~kie~~G~~YelGDF~VrvG~Vt~~-~~~rGilvEVEY~ 116 (118)
|+.++.-.+. -.+.-+-.-|++||.++=-. ...+ =+-|-+.+||.|.
T Consensus 10 F~~V~~G~Kt-------fEiRkNDRdf~VGD~L~L~E-~~~~~YTGr~~~~~Ityi 57 (72)
T PF12961_consen 10 FEAVLSGRKT-------FEIRKNDRDFQVGDILVLRE-WDNGEYTGREIEAEITYI 57 (72)
T ss_pred HHHHHCCCce-------EEEEecCCCCCCCCEEEEEE-ecCCCccccEEEEEEEEE
Confidence 4555554444 23333455699999876432 3323 2566778888775
No 20
>PF00366 Ribosomal_S17: Ribosomal protein S17; InterPro: IPR000266 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 [, ]. The ribosomal proteins catalyse ribosome assembly and stabilise the rRNA, tuning the structure of the ribosome for optimal function. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S17 is known to bind specifically to the 5' end of 16S ribosomal RNA in Escherichia coli (primary rRNA binding protein), and is thought to be involved in the recognition of termination codons. Experimental evidence [] has revealed that S17 has virtually no groups exposed on the ribosomal surface.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_Q 2VHP_Q 3BBN_Q 2QAL_Q 3OAR_Q 1VS5_Q 3KC4_Q 2AW7_Q 3E1C_J 2AVY_Q ....
Probab=21.96 E-value=82 Score=20.73 Aligned_cols=59 Identities=24% Similarity=0.270 Sum_probs=31.2
Q ss_pred eeeeeeecchHHHHHHhcccceeeccceEEEEccceeEeCCeEEEEeee-EecCcccEEEEEE
Q psy8505 52 KNIPVVADSLFDLLMMKMTPVYTSKKQTKVESKGPRFELGDFCVKLGSV-SISQNFKAVLVEV 113 (118)
Q Consensus 52 k~~~l~aD~~fd~im~kL~s~y~~r~~~kie~~G~~YelGDF~VrvG~V-t~~~~~rGilvEV 113 (118)
|++.+..+..+- -.+.+-....++.-.+--+...-++||. |++... -.+.+.+++++||
T Consensus 10 KTv~V~v~~~~~--~~ky~K~~~~~kk~~aHD~~~~~~vGD~-V~I~e~rPiSk~K~~~v~~v 69 (69)
T PF00366_consen 10 KTVVVRVERLVY--HPKYKKYIKRTKKYMAHDENNICKVGDK-VRIRECRPISKTKRFVVVEV 69 (69)
T ss_dssp TEEEEEEEEEEE--ETTTEEEEEEEEEEEEE-TTSSSTTTSE-EEEEEEEEEETTEEEEEEEE
T ss_pred CeEEEEEEEEEE--cceEeeccCccccEEEeCCccCCCCCCE-EEEEeeeccCCcEeEEEEEC
Confidence 566666665541 2233332222222122223333457884 566555 5778999999997
No 21
>PF13856 Gifsy-2: ATP-binding sugar transporter from pro-phage; PDB: 2PP6_A.
Probab=21.37 E-value=47 Score=22.56 Aligned_cols=31 Identities=19% Similarity=0.295 Sum_probs=25.5
Q ss_pred cchHHHHHHhcccceeeccceEEEEccceeE
Q psy8505 59 DSLFDLLMMKMTPVYTSKKQTKVESKGPRFE 89 (118)
Q Consensus 59 D~~fd~im~kL~s~y~~r~~~kie~~G~~Ye 89 (118)
++.||.++..+.......-+..+.++|..|.
T Consensus 2 ~~~fd~~~~d~D~~~~~~fg~~~~InG~~~~ 32 (95)
T PF13856_consen 2 ASFFDQLAADIDAVILDEFGEEHTINGKPYR 32 (95)
T ss_dssp HHHHHHHHHHHHHHHHHHH-EEEEETTEEEE
T ss_pred CCHHHHHHHHHHHHHHHHhCCeEEECCEEEE
Confidence 4678999999998888888888999998777
No 22
>cd04715 BAH_Orc1p_like BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of Saccharomyces cerevisiae Orc1p and similar proteins. Orc1 is part of the Yeast Sir1-origin recognition complex, the Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=21.31 E-value=81 Score=23.98 Aligned_cols=33 Identities=15% Similarity=0.267 Sum_probs=21.6
Q ss_pred EEEEccceeEeCCeEE-EEeeeEecCcccEEEEEEEE
Q psy8505 80 KVESKGPRFELGDFCV-KLGSVSISQNFKAVLVEVRT 115 (118)
Q Consensus 80 kie~~G~~YelGDF~V-rvG~Vt~~~~~rGilvEVEY 115 (118)
++.++|..|++||+.. +-+. ++..=|.|+++.-
T Consensus 22 s~~~~g~~y~lGD~Vlv~s~~---~~~yIgkI~~iwe 55 (159)
T cd04715 22 SFTYDGVEYRLYDDVYVHNGD---SEPYIGKIIKIYE 55 (159)
T ss_pred EEEECCEEEeCCCEEEEeCCC---CCCEEEEEEEEEE
Confidence 4889999999999753 3222 3455566666543
No 23
>PF08940 DUF1918: Domain of unknown function (DUF1918); InterPro: IPR015035 This domain is found in various hypothetical bacterial proteins, and has no known function. ; PDB: 2A7Y_A.
Probab=20.28 E-value=31 Score=22.72 Aligned_cols=25 Identities=28% Similarity=0.278 Sum_probs=13.2
Q ss_pred EeCCeEEEEeeeEecCcccEEEEEE
Q psy8505 89 ELGDFCVKLGSVSISQNFKAVLVEV 113 (118)
Q Consensus 89 elGDF~VrvG~Vt~~~~~rGilvEV 113 (118)
+.||++|-=|...-...-+|.|+||
T Consensus 4 ~vGD~lvv~g~~vg~~~r~GeIveV 28 (58)
T PF08940_consen 4 SVGDRLVVHGRTVGQPDRHGEIVEV 28 (58)
T ss_dssp -TTEEEEES-TTTS--EEEEEEEE-
T ss_pred CCCCEEEEcCCcCCCCCcEeEEEEE
Confidence 3577776665554445667777776
Done!