Query psy11271
Match_columns 78
No_of_seqs 111 out of 171
Neff 3.6
Searched_HMMs 46136
Date Fri Aug 16 22:37:25 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11271.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11271hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3499|consensus 100.0 2.5E-45 5.5E-50 233.3 7.9 69 1-77 1-69 (69)
2 PTZ00181 60S ribosomal protein 100.0 1.3E-43 2.8E-48 232.2 8.5 69 1-77 1-69 (82)
3 PF01781 Ribosomal_L38e: Ribos 100.0 9.8E-43 2.1E-47 221.8 6.8 68 2-77 1-69 (69)
4 PTZ00193 60S ribosomal protein 73.5 5.7 0.00012 29.8 3.8 50 2-55 106-171 (188)
5 PRK06302 acetyl-CoA carboxylas 58.2 20 0.00044 25.0 4.0 24 5-28 3-26 (155)
6 PTZ00039 40S ribosomal protein 57.3 60 0.0013 22.2 6.1 65 8-75 35-112 (115)
7 TIGR00531 BCCP acetyl-CoA carb 55.2 24 0.00053 24.7 4.0 25 4-28 2-26 (156)
8 PF14227 UBN2_2: gag-polypepti 39.7 16 0.00034 23.2 1.0 19 54-72 61-79 (119)
9 PF14223 UBN2: gag-polypeptide 39.1 20 0.00043 22.7 1.4 20 54-73 63-82 (119)
10 COG4269 Predicted membrane pro 33.6 6.1 0.00013 32.3 -2.0 10 43-52 49-58 (364)
11 TIGR01451 B_ant_repeat conserv 33.6 14 0.00029 21.5 -0.0 30 46-75 11-44 (53)
12 KOG3346|consensus 32.8 26 0.00056 25.9 1.3 14 46-59 61-74 (185)
13 PRK12271 rps10p 30S ribosomal 31.9 1.6E+02 0.0034 19.6 7.1 65 8-75 20-97 (102)
14 PF00703 Glyco_hydro_2: Glycos 29.1 38 0.00082 20.0 1.4 10 47-56 83-92 (110)
15 PF12746 GNAT_acetyltran: GNAT 28.5 35 0.00076 26.1 1.4 32 46-77 101-134 (265)
16 PF10105 DUF2344: Uncharacteri 27.8 59 0.0013 23.4 2.4 20 58-77 75-94 (187)
17 PF08671 SinI: Anti-repressor 26.4 55 0.0012 17.7 1.6 12 4-15 18-29 (30)
18 cd01812 BAG1_N Ubiquitin-like 25.4 1.1E+02 0.0023 17.4 2.9 28 41-68 2-29 (71)
19 TIGR01046 S10_Arc_S20_Euk ribo 24.0 2.2E+02 0.0048 18.7 7.2 65 8-75 19-96 (99)
20 PF06470 SMC_hinge: SMC protei 23.9 28 0.00062 21.6 0.2 23 47-69 27-49 (120)
21 PF01345 DUF11: Domain of unkn 23.5 25 0.00054 20.8 -0.1 27 49-75 43-73 (76)
22 PRK10598 lipoprotein; Provisio 22.1 74 0.0016 23.5 2.1 24 51-75 153-176 (186)
No 1
>KOG3499|consensus
Probab=100.00 E-value=2.5e-45 Score=233.28 Aligned_cols=69 Identities=78% Similarity=1.191 Sum_probs=67.8
Q ss_pred CchhhHHHHHHHHHhhhCCCceeEEeccccCCCCCCCCceeEEEeecCcEEEEEecChHHHHHhHhcCCCCCeeeec
Q psy11271 1 MPREIKEIKEFLLKARRKDAKSVTIKRNISKNKDKKPDNTKFKVRCSRFLYTLVITDNEKAEKLKQSLPPGLQVKEI 77 (78)
Q Consensus 1 MPkeI~dIK~Fl~~arrkDAksv~IKk~~~~~~~~~~~~tKFKvRcsryLYTLvv~D~eKAeKl~qSLPP~l~v~~~ 77 (78)
||+||+|||+||++|||+||+||+||+| +++||||||||||||||||.|++|||||+|||||||+|+|+
T Consensus 1 Mpr~i~eiK~FL~~arR~Da~s~kiKkn--------~~~~KFKvRcsryLYTLvv~D~~KAeKlkQSLPP~l~V~el 69 (69)
T KOG3499|consen 1 MPRQITEIKDFLLTARRKDAKSVKIKKN--------KNNVKFKVRCSRYLYTLVVADAEKAEKLKQSLPPGLTVKEL 69 (69)
T ss_pred CcchHHHHHHHHHHHHhcccceeEEEec--------CCceeEEEEeeeeeeeeeeccHHHHHHHHhcCCCCceeecC
Confidence 9999999999999999999999999999 88999999999999999999999999999999999999985
No 2
>PTZ00181 60S ribosomal protein L38; Provisional
Probab=100.00 E-value=1.3e-43 Score=232.24 Aligned_cols=69 Identities=55% Similarity=0.945 Sum_probs=67.9
Q ss_pred CchhhHHHHHHHHHhhhCCCceeEEeccccCCCCCCCCceeEEEeecCcEEEEEecChHHHHHhHhcCCCCCeeeec
Q psy11271 1 MPREIKEIKEFLLKARRKDAKSVTIKRNISKNKDKKPDNTKFKVRCSRFLYTLVITDNEKAEKLKQSLPPGLQVKEI 77 (78)
Q Consensus 1 MPkeI~dIK~Fl~~arrkDAksv~IKk~~~~~~~~~~~~tKFKvRcsryLYTLvv~D~eKAeKl~qSLPP~l~v~~~ 77 (78)
||+||+|||+||++|||+||+||+||+| .++||||||||||||||+|+|.+||+||+|||||||+|+++
T Consensus 1 MPkeI~dIK~FL~~arrkDAksvkIKkn--------~~~tKFKvRcsrYLYTLvv~D~~KA~KlkqSLPp~l~v~~v 69 (82)
T PTZ00181 1 MPREIKTLKEFLAICSRKDARCVKVKHN--------PSATKFKVRCSRYLYTLVVADKKKADKIERSIHPSVKKITV 69 (82)
T ss_pred CchhHHHHHHHHHHhhccCceEEEeecC--------CcceEEEEEecceEEEEEeCCHHHHHHHHhcCCCCceEEEe
Confidence 9999999999999999999999999999 89999999999999999999999999999999999999986
No 3
>PF01781 Ribosomal_L38e: Ribosomal L38e protein family; InterPro: IPR002675 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 L38e forms part of the 60S ribosomal subunit []. This family is found in eukaryotes.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_n 3IZR_n 4A1D_P 4A19_P 4A18_P 4A1B_P.
Probab=100.00 E-value=9.8e-43 Score=221.82 Aligned_cols=68 Identities=79% Similarity=1.195 Sum_probs=62.2
Q ss_pred chhhHHHHHHHHHhhhCCCceeEEeccccCCCCCCCCc-eeEEEeecCcEEEEEecChHHHHHhHhcCCCCCeeeec
Q psy11271 2 PREIKEIKEFLLKARRKDAKSVTIKRNISKNKDKKPDN-TKFKVRCSRFLYTLVITDNEKAEKLKQSLPPGLQVKEI 77 (78)
Q Consensus 2 PkeI~dIK~Fl~~arrkDAksv~IKk~~~~~~~~~~~~-tKFKvRcsryLYTLvv~D~eKAeKl~qSLPP~l~v~~~ 77 (78)
|+||+|||+||++|||+||+||+||+| +++ ||||||||||||||+|+|+||||+|+|||||||.+++|
T Consensus 1 Pkqi~~iK~FL~~arrkDAksv~iKk~--------~~~~tKFKvRcsryLYTLvv~d~~KAeklkqSLPp~l~v~~i 69 (69)
T PF01781_consen 1 PKQIKDIKDFLETARRKDAKSVKIKKN--------KDNGTKFKVRCSRYLYTLVVKDKEKAEKLKQSLPPGLKVKEI 69 (69)
T ss_dssp -THHHHHHHHHHHHCSS-EEEEEEECE--------SSSTEEEEEECSS-EEEESS-SHHHHHHHHHSSSSSSEEEEE
T ss_pred CcchhhHHHHHHHHhhCCCceEEEEec--------CCCeeEEEEEecceEEEEEEcCHHHHHHHHhhCCCCCeEeeC
Confidence 899999999999999999999999999 666 99999999999999999999999999999999999986
No 4
>PTZ00193 60S ribosomal protein L31; Provisional
Probab=73.51 E-value=5.7 Score=29.84 Aligned_cols=50 Identities=28% Similarity=0.355 Sum_probs=34.2
Q ss_pred chhhHHHHHHHHHhhhCCCceeEEeccccCCC----CC-CCCceeEEEeecCc-----------EEEEEe
Q psy11271 2 PREIKEIKEFLLKARRKDAKSVTIKRNISKNK----DK-KPDNTKFKVRCSRF-----------LYTLVI 55 (78)
Q Consensus 2 PkeI~dIK~Fl~~arrkDAksv~IKk~~~~~~----~~-~~~~tKFKvRcsry-----------LYTLvv 55 (78)
|+-|.+|+.|+.-.. +...|+|=-. .|. .| .+.-.++.||.||. ||||+-
T Consensus 106 PrAIKeIRkFA~K~M--gT~DVRIDtr--LNkaIWsrGIRnvP~RIRVRlsRKrNedEDs~~KklYTlVt 171 (188)
T PTZ00193 106 PIAIKRIKAFVGRLM--KTKDNRIDAS--LNTYIWHKGVKGVPGRVRVLVERKSETLEGGKRKHFYTVIS 171 (188)
T ss_pred HHHHHHHHHHHHHhc--CCCcEEECHH--HHHHHHHccCcCCCceEEEEEEeecCccccCcccceEEEEE
Confidence 788999999988876 6777887432 110 01 12246888999985 898874
No 5
>PRK06302 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=58.17 E-value=20 Score=24.98 Aligned_cols=24 Identities=21% Similarity=0.336 Sum_probs=22.2
Q ss_pred hHHHHHHHHHhhhCCCceeEEecc
Q psy11271 5 IKEIKEFLLKARRKDAKSVTIKRN 28 (78)
Q Consensus 5 I~dIK~Fl~~arrkDAksv~IKk~ 28 (78)
+++|++.+.+..+.|..++.++..
T Consensus 3 ~~~I~~Li~~~~~s~l~ele~~~~ 26 (155)
T PRK06302 3 IRKIKKLIELVDESGISEFEIKEG 26 (155)
T ss_pred HHHHHHHHHHHHHCCCeEEEEEcC
Confidence 679999999999999999999876
No 6
>PTZ00039 40S ribosomal protein S20; Provisional
Probab=57.34 E-value=60 Score=22.22 Aligned_cols=65 Identities=15% Similarity=0.343 Sum_probs=44.2
Q ss_pred HHHHHHHhhhCCCce------------eEEeccccCCCCCCCCceeEEEeecCcEEEEEecChHHHHHhH-hcCCCCCee
Q psy11271 8 IKEFLLKARRKDAKS------------VTIKRNISKNKDKKPDNTKFKVRCSRFLYTLVITDNEKAEKLK-QSLPPGLQV 74 (78)
Q Consensus 8 IK~Fl~~arrkDAks------------v~IKk~~~~~~~~~~~~tKFKvRcsryLYTLvv~D~eKAeKl~-qSLPP~l~v 74 (78)
.++|+++|++.+|+- +.+-++ ...++++.--.|..|.-+=|.-|.-+ .+-++.|. .+||||..|
T Consensus 35 ~~~Ii~~ak~~g~~v~GPipLPtK~~~~tvlrS--Phg~~kksreqfE~RiHKRlIdI~~~-~~~v~~l~~~~lp~GV~I 111 (115)
T PTZ00039 35 CADIITGAKEKNLKVTGPVRMPVKTLRITTRKS--PCGEGTNTWDRFEMRIYKRVIDLYSS-SDVVTQITSINIDPGVEV 111 (115)
T ss_pred HHHHHHHHHHcCCEeECCccCCceeEEEEeeeC--CCCCCCchHHHheeeeeeEEEEEeCC-HHHHHHHhCCCCCCCcEE
Confidence 467888999887753 223333 33333333457999999988888654 55578866 689999987
Q ss_pred e
Q psy11271 75 K 75 (78)
Q Consensus 75 ~ 75 (78)
.
T Consensus 112 e 112 (115)
T PTZ00039 112 E 112 (115)
T ss_pred E
Confidence 5
No 7
>TIGR00531 BCCP acetyl-CoA carboxylase, biotin carboxyl carrier protein. The gene name is accB or fabE.
Probab=55.15 E-value=24 Score=24.66 Aligned_cols=25 Identities=24% Similarity=0.418 Sum_probs=22.7
Q ss_pred hhHHHHHHHHHhhhCCCceeEEecc
Q psy11271 4 EIKEIKEFLLKARRKDAKSVTIKRN 28 (78)
Q Consensus 4 eI~dIK~Fl~~arrkDAksv~IKk~ 28 (78)
.+++|++.+.+..+.+..++.|+.+
T Consensus 2 d~~~Ik~Li~~~~~s~l~elei~~~ 26 (156)
T TIGR00531 2 NIREIKELIKLIEESGITELELKEE 26 (156)
T ss_pred CHHHHHHHHHHHHHCCCcEEEEEeC
Confidence 3689999999999999999999876
No 8
>PF14227 UBN2_2: gag-polypeptide of LTR copia-type
Probab=39.68 E-value=16 Score=23.19 Aligned_cols=19 Identities=42% Similarity=0.578 Sum_probs=16.9
Q ss_pred EecChHHHHHhHhcCCCCC
Q psy11271 54 VITDNEKAEKLKQSLPPGL 72 (78)
Q Consensus 54 vv~D~eKAeKl~qSLPP~l 72 (78)
.++|.+.+.-|..||||..
T Consensus 61 ~i~d~~~~~~lL~sLP~sy 79 (119)
T PF14227_consen 61 PIDDEDKVIILLSSLPPSY 79 (119)
T ss_pred cchHHHHHHHHHHcCCHhH
Confidence 4789999999999999974
No 9
>PF14223 UBN2: gag-polypeptide of LTR copia-type
Probab=39.07 E-value=20 Score=22.74 Aligned_cols=20 Identities=35% Similarity=0.639 Sum_probs=17.7
Q ss_pred EecChHHHHHhHhcCCCCCe
Q psy11271 54 VITDNEKAEKLKQSLPPGLQ 73 (78)
Q Consensus 54 vv~D~eKAeKl~qSLPP~l~ 73 (78)
.+.|.+...++..||||...
T Consensus 63 ~i~d~~~v~~iL~~Lp~~y~ 82 (119)
T PF14223_consen 63 PISDEDLVSKILRSLPPSYD 82 (119)
T ss_pred cccchhHHHHHHhcCCchhH
Confidence 57899999999999999764
No 10
>COG4269 Predicted membrane protein [Function unknown]
Probab=33.59 E-value=6.1 Score=32.27 Aligned_cols=10 Identities=50% Similarity=0.913 Sum_probs=9.0
Q ss_pred EEeecCcEEE
Q psy11271 43 KVRCSRFLYT 52 (78)
Q Consensus 43 KvRcsryLYT 52 (78)
||||.||+|+
T Consensus 49 ~VR~rrYfYg 58 (364)
T COG4269 49 KVRRRRYFYG 58 (364)
T ss_pred HHHHHHhhhc
Confidence 6899999996
No 11
>TIGR01451 B_ant_repeat conserved repeat domain. This model represents the conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis, and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydial outer membrane proteins.
Probab=33.56 E-value=14 Score=21.48 Aligned_cols=30 Identities=23% Similarity=0.416 Sum_probs=20.1
Q ss_pred ecCcEEEEEecChHHHH----HhHhcCCCCCeee
Q psy11271 46 CSRFLYTLVITDNEKAE----KLKQSLPPGLQVK 75 (78)
Q Consensus 46 csryLYTLvv~D~eKAe----Kl~qSLPP~l~v~ 75 (78)
+...-|||.+.+..-+. .+...||+|+...
T Consensus 11 Gd~v~Yti~v~N~g~~~a~~v~v~D~lP~g~~~v 44 (53)
T TIGR01451 11 GDTITYTITVTNNGNVPATNVVVTDILPSGTTFV 44 (53)
T ss_pred CCEEEEEEEEEECCCCceEeEEEEEcCCCCCEEE
Confidence 44456788887665443 3677899998764
No 12
>KOG3346|consensus
Probab=32.84 E-value=26 Score=25.88 Aligned_cols=14 Identities=50% Similarity=0.634 Sum_probs=13.1
Q ss_pred ecCcEEEEEecChH
Q psy11271 46 CSRFLYTLVITDNE 59 (78)
Q Consensus 46 csryLYTLvv~D~e 59 (78)
+.+-||||++.|++
T Consensus 61 ~~~~~yTLvm~DPD 74 (185)
T KOG3346|consen 61 DPGSLYTLVMTDPD 74 (185)
T ss_pred CCCCeEEEEEeCCC
Confidence 89999999999986
No 13
>PRK12271 rps10p 30S ribosomal protein S10P; Reviewed
Probab=31.91 E-value=1.6e+02 Score=19.60 Aligned_cols=65 Identities=12% Similarity=0.235 Sum_probs=44.3
Q ss_pred HHHHHHHhhhCCCce------------eEEeccccCCCCCCCCceeEEEeecCcEEEEEecChHHHHHhH-hcCCCCCee
Q psy11271 8 IKEFLLKARRKDAKS------------VTIKRNISKNKDKKPDNTKFKVRCSRFLYTLVITDNEKAEKLK-QSLPPGLQV 74 (78)
Q Consensus 8 IK~Fl~~arrkDAks------------v~IKk~~~~~~~~~~~~tKFKvRcsryLYTLvv~D~eKAeKl~-qSLPP~l~v 74 (78)
.++++++|++.+|+- +.+-++ ...++++.-=.|.+|.-+=|.-| ..+.+-++.|. ..||||+.+
T Consensus 20 ~~~I~~~~k~~g~~~~GPipLPtk~~~~tv~rS--Ph~~gk~sreqfE~r~hKRlidi-~~~~~~~~~l~~~~lp~gV~i 96 (102)
T PRK12271 20 CDQIKEIAEKTGVDMSGPIPLPTKRLVVPTRKS--PDGEGTATWDHWEMRIHKRLIDI-DADERALRQLMRIRVPEDVQI 96 (102)
T ss_pred HHHHHHHHHHcCCeEECCCcCCceeEEEEeeeC--CCCCCCcchHHeEEEEeEEEEEe-eCCHHHHHHHhCCCCCCCcEE
Confidence 467888899888743 223333 33333333347999999999888 56677777765 679999987
Q ss_pred e
Q psy11271 75 K 75 (78)
Q Consensus 75 ~ 75 (78)
.
T Consensus 97 e 97 (102)
T PRK12271 97 E 97 (102)
T ss_pred E
Confidence 4
No 14
>PF00703 Glyco_hydro_2: Glycosyl hydrolases family 2; InterPro: IPR006102 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 2 GH2 from CAZY comprises enzymes with several known activities: beta-galactosidase (3.2.1.23 from EC); beta-mannosidase (3.2.1.25 from EC); beta-glucuronidase (3.2.1.31 from EC). These enzymes contain a conserved glutamic acid residue which has been shown [], in Escherichia coli lacZ (P00722 from SWISSPROT), to be the general acid/base catalyst in the active site of the enzyme. This entry describes the immunoglobulin-like beta-sandwich domain [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3FN9_C 3DEC_A 3OB8_A 3OBA_A 3CMG_A 3GM8_A 3HN3_E 1BHG_A 2VZU_A 2X09_A ....
Probab=29.06 E-value=38 Score=20.03 Aligned_cols=10 Identities=40% Similarity=0.803 Sum_probs=7.5
Q ss_pred cCcEEEEEec
Q psy11271 47 SRFLYTLVIT 56 (78)
Q Consensus 47 sryLYTLvv~ 56 (78)
.-|||+|.+.
T Consensus 83 ~P~LY~l~v~ 92 (110)
T PF00703_consen 83 DPYLYTLEVE 92 (110)
T ss_dssp SBSEEEEEEE
T ss_pred CceEEEEEEE
Confidence 4589998875
No 15
>PF12746 GNAT_acetyltran: GNAT acetyltransferase; PDB: 3G3S_B.
Probab=28.46 E-value=35 Score=26.12 Aligned_cols=32 Identities=31% Similarity=0.539 Sum_probs=21.0
Q ss_pred ecCcEEEEEec--ChHHHHHhHhcCCCCCeeeec
Q psy11271 46 CSRFLYTLVIT--DNEKAEKLKQSLPPGLQVKEI 77 (78)
Q Consensus 46 csryLYTLvv~--D~eKAeKl~qSLPP~l~v~~~ 77 (78)
-.||.|+..-. |.++-+++..+||.+..+..|
T Consensus 101 ~~Ry~~~~~~~~Fd~~~l~~~~~~lp~~y~l~~I 134 (265)
T PF12746_consen 101 FTRYAFKKEPEVFDKEKLKKYVSALPEGYELKRI 134 (265)
T ss_dssp EEEEEE-SS-----HHHHHHHHHCS-TTCEEEE-
T ss_pred eeeeeeeeccccccHHHHHHHHhcCCCCeEEEEC
Confidence 46888886443 677778888899999998765
No 16
>PF10105 DUF2344: Uncharacterized protein conserved in bacteria (DUF2344); InterPro: IPR018768 This domain, found in various hypothetical bacterial proteins and Radical Sam domain proteins, has no known function.
Probab=27.75 E-value=59 Score=23.35 Aligned_cols=20 Identities=40% Similarity=0.642 Sum_probs=16.8
Q ss_pred hHHHHHhHhcCCCCCeeeec
Q psy11271 58 NEKAEKLKQSLPPGLQVKEI 77 (78)
Q Consensus 58 ~eKAeKl~qSLPP~l~v~~~ 77 (78)
.+-.++|.+.||+|+.+.++
T Consensus 75 ~~~~~rLn~~lP~Gl~i~~~ 94 (187)
T PF10105_consen 75 EEVLERLNAVLPEGLRILEA 94 (187)
T ss_pred HHHHHHHHHhCCCCCEEEEE
Confidence 46678899999999999764
No 17
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=26.42 E-value=55 Score=17.71 Aligned_cols=12 Identities=42% Similarity=0.495 Sum_probs=9.0
Q ss_pred hhHHHHHHHHHh
Q psy11271 4 EIKEIKEFLLKA 15 (78)
Q Consensus 4 eI~dIK~Fl~~a 15 (78)
.++||++||+..
T Consensus 18 s~eeir~FL~~~ 29 (30)
T PF08671_consen 18 SKEEIREFLEFN 29 (30)
T ss_dssp -HHHHHHHHHHH
T ss_pred CHHHHHHHHHhC
Confidence 478999999763
No 18
>cd01812 BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).
Probab=25.42 E-value=1.1e+02 Score=17.41 Aligned_cols=28 Identities=21% Similarity=0.240 Sum_probs=21.1
Q ss_pred eEEEeecCcEEEEEecChHHHHHhHhcC
Q psy11271 41 KFKVRCSRFLYTLVITDNEKAEKLKQSL 68 (78)
Q Consensus 41 KFKvRcsryLYTLvv~D~eKAeKl~qSL 68 (78)
++.||.+...|++.|.+.+-...|++.+
T Consensus 2 ~i~vk~~g~~~~i~v~~~~tv~~lK~~i 29 (71)
T cd01812 2 RVRVKHGGESHDLSISSQATFGDLKKML 29 (71)
T ss_pred EEEEEECCEEEEEEECCCCcHHHHHHHH
Confidence 4567777778888888877777777764
No 19
>TIGR01046 S10_Arc_S20_Euk ribosomal protein S10(archaeal)/S20(eukaryotic). its equivalents in eukaryotes.
Probab=23.97 E-value=2.2e+02 Score=18.70 Aligned_cols=65 Identities=11% Similarity=0.255 Sum_probs=43.3
Q ss_pred HHHHHHHhhhCCCce------------eEEeccccCCCCCCCCceeEEEeecCcEEEEEecChHHHHHhH-hcCCCCCee
Q psy11271 8 IKEFLLKARRKDAKS------------VTIKRNISKNKDKKPDNTKFKVRCSRFLYTLVITDNEKAEKLK-QSLPPGLQV 74 (78)
Q Consensus 8 IK~Fl~~arrkDAks------------v~IKk~~~~~~~~~~~~tKFKvRcsryLYTLvv~D~eKAeKl~-qSLPP~l~v 74 (78)
.+++++.|++.+++- +.+-++ .-+++++.-=.|.+|.-+=|.-|.- +.+-++.|. ..||||..|
T Consensus 19 ~~~I~~~ak~~g~~~~GPipLPtk~~~~tv~rs--Ph~~~~ks~e~fE~r~hKRlidi~~-~~~~~~~l~~~~lp~gV~v 95 (99)
T TIGR01046 19 CAQIKRIAEKTGVRMSGPVPLPTKRLRVPTRKS--PDGEGSKTWDRWEMRIHKRLIDIEA-DERALRQIMRISVPEDVEI 95 (99)
T ss_pred HHHHHHHHHHcCCEEECCccCCcceEEEEeeeC--CCCCCCcchHheEEEEEEEEEEEEC-CHHHHHHHhCCCCCCCcEE
Confidence 467888888887753 223333 2222222223799999998888864 467777766 689999987
Q ss_pred e
Q psy11271 75 K 75 (78)
Q Consensus 75 ~ 75 (78)
.
T Consensus 96 e 96 (99)
T TIGR01046 96 E 96 (99)
T ss_pred E
Confidence 4
No 20
>PF06470 SMC_hinge: SMC proteins Flexible Hinge Domain; InterPro: IPR010935 This entry represents the hinge region of the SMC (Structural Maintenance of Chromosomes) family of proteins. The hinge region is responsible for formation of the DNA interacting dimer. It is also possible that the precise structure of it is an essential determinant of the specificity of the DNA-protein interaction [].; GO: 0005515 protein binding, 0005524 ATP binding, 0051276 chromosome organization, 0005694 chromosome; PDB: 2WD5_A 1GXL_C 1GXK_A 1GXJ_A 3NWC_B 3L51_A.
Probab=23.91 E-value=28 Score=21.60 Aligned_cols=23 Identities=30% Similarity=0.398 Sum_probs=19.6
Q ss_pred cCcEEEEEecChHHHHHhHhcCC
Q psy11271 47 SRFLYTLVITDNEKAEKLKQSLP 69 (78)
Q Consensus 47 sryLYTLvv~D~eKAeKl~qSLP 69 (78)
+.||.+++|.|.+-|.++.+.|.
T Consensus 27 G~~l~~iVV~~~~~a~~~i~~l~ 49 (120)
T PF06470_consen 27 GGRLQAIVVEDEETAKKIIEFLK 49 (120)
T ss_dssp GGGGGSEEESSHHHHHHHHHHHH
T ss_pred HHhhceEEECcHHHHHHHHHHHh
Confidence 56889999999999998877665
No 21
>PF01345 DUF11: Domain of unknown function DUF11; InterPro: IPR001434 This group of sequences is represented by a conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis (Streptococcus faecalis), and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydia trachomatis outer membrane proteins. In C. trachomatis, three cysteine-rich proteins (also believed to be lipoproteins), MOMP, OMP6 and OMP3, make up the extracellular matrix of the outer membrane []. They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. They are thought to be involved in porin formation and, as these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism.; GO: 0005727 extrachromosomal circular DNA
Probab=23.51 E-value=25 Score=20.81 Aligned_cols=27 Identities=30% Similarity=0.546 Sum_probs=16.0
Q ss_pred cEEEEEecChHHHH----HhHhcCCCCCeee
Q psy11271 49 FLYTLVITDNEKAE----KLKQSLPPGLQVK 75 (78)
Q Consensus 49 yLYTLvv~D~eKAe----Kl~qSLPP~l~v~ 75 (78)
.-|||.|.+..-+. .|...||+||...
T Consensus 43 v~ytitvtN~G~~~a~nv~v~D~lp~g~~~v 73 (76)
T PF01345_consen 43 VTYTITVTNTGPAPATNVVVTDTLPAGLTFV 73 (76)
T ss_pred EEEEEEEEECCCCeeEeEEEEEcCCCCCEEe
Confidence 34666665443222 3557889998764
No 22
>PRK10598 lipoprotein; Provisional
Probab=22.07 E-value=74 Score=23.49 Aligned_cols=24 Identities=50% Similarity=0.722 Sum_probs=19.0
Q ss_pred EEEEecChHHHHHhHhcCCCCCeee
Q psy11271 51 YTLVITDNEKAEKLKQSLPPGLQVK 75 (78)
Q Consensus 51 YTLvv~D~eKAeKl~qSLPP~l~v~ 75 (78)
|+|- +|.+++|.|..+++++|.|+
T Consensus 153 Y~L~-d~~~~~eal~kk~~k~i~Vk 176 (186)
T PRK10598 153 YVLR-EDKSKAEALAKKLAKGLEVK 176 (186)
T ss_pred EEEC-CCCCHHHHHHHhccCCCEEE
Confidence 5552 44788999999999999886
Done!