Query psy12837
Match_columns 184
No_of_seqs 122 out of 864
Neff 2.8
Searched_HMMs 46136
Date Fri Aug 16 21:03:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12837.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12837hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0292 RplT Ribosomal protein 100.0 6.9E-34 1.5E-38 223.2 7.5 72 26-97 47-118 (118)
2 PTZ00030 60S ribosomal protein 100.0 3.1E-33 6.6E-38 219.6 8.2 80 18-97 21-109 (121)
3 PRK05185 rplT 50S ribosomal pr 100.0 5.6E-33 1.2E-37 215.8 7.3 76 18-93 29-113 (114)
4 TIGR01032 rplT_bact ribosomal 100.0 7.2E-33 1.6E-37 215.1 7.2 76 18-93 29-113 (113)
5 CHL00068 rpl20 ribosomal prote 100.0 2.3E-32 5E-37 213.0 7.9 76 18-93 30-114 (115)
6 PRK14537 50S ribosomal protein 100.0 2.2E-31 4.7E-36 227.6 8.5 89 18-106 30-128 (230)
7 PF00453 Ribosomal_L20: Riboso 100.0 1.8E-31 3.9E-36 205.4 6.4 71 18-88 29-108 (108)
8 KOG4707|consensus 99.8 3E-22 6.5E-27 162.4 2.9 72 23-94 51-122 (147)
9 KOG1255|consensus 91.4 0.11 2.4E-06 47.3 1.8 57 109-171 24-84 (329)
10 COG3514 Uncharacterized protei 59.2 3.7 8E-05 32.0 0.4 14 38-51 75-88 (93)
11 PTZ00187 succinyl-CoA syntheta 55.8 4.8 0.0001 36.5 0.6 37 108-146 14-51 (317)
12 PF05225 HTH_psq: helix-turn-h 34.3 23 0.0005 23.2 1.1 21 44-64 19-39 (45)
13 PF12668 DUF3791: Protein of u 32.3 78 0.0017 21.7 3.6 55 41-97 5-59 (62)
14 PF11527 ARL2_Bind_BART: The A 28.9 1.2E+02 0.0025 23.2 4.4 60 34-93 51-114 (121)
15 PF14384 DUF4415: Domain of un 27.5 29 0.00064 24.1 0.8 12 40-51 50-61 (62)
16 PF03683 UPF0175: Uncharacteri 26.0 69 0.0015 22.9 2.5 27 44-70 37-63 (76)
17 PF00126 HTH_1: Bacterial regu 25.7 65 0.0014 21.4 2.2 28 43-70 15-42 (60)
18 PRK03573 transcriptional regul 24.6 3.1E+02 0.0067 20.6 7.3 58 35-92 11-70 (144)
19 PRK13858 type IV secretion sys 22.9 1.9E+02 0.0042 24.1 4.9 98 18-118 6-114 (147)
20 PF01527 HTH_Tnp_1: Transposas 22.0 61 0.0013 21.7 1.5 24 42-65 24-47 (76)
21 PF03050 DDE_Tnp_IS66: Transpo 21.9 1E+02 0.0022 25.6 3.2 64 50-119 18-81 (271)
22 PF15410 PH_9: Pleckstrin homo 21.6 50 0.0011 25.0 1.1 11 38-48 108-118 (119)
23 PRK01905 DNA-binding protein F 21.3 80 0.0017 22.5 2.1 25 43-67 52-76 (77)
24 PF07818 HCNGP: HCNGP-like pro 21.2 1E+02 0.0022 23.5 2.7 38 55-93 17-54 (96)
25 cd06093 PX_domain The Phox Hom 20.5 58 0.0013 22.2 1.2 25 3-29 17-41 (106)
26 smart00216 VWD von Willebrand 20.0 42 0.0009 25.5 0.4 13 6-18 18-30 (162)
No 1
>COG0292 RplT Ribosomal protein L20 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.9e-34 Score=223.20 Aligned_cols=72 Identities=33% Similarity=0.569 Sum_probs=70.5
Q ss_pred hchhhhhhhhhHHHHHHHHHhhhccCCCChHHHHHHHHHCCcccchhHHHHHHhcChhHHHHHHHHHHHHHh
Q psy12837 26 CNEEINLTGHIGKLWTARITAGAEEHGVPYPLFREGLTRSNIMLDRKTLSDLAAWEPRTFKVKKSTVGTTMC 97 (184)
Q Consensus 26 yRDRKkKKRdFRrLWItRINAAaRe~GisYSkFI~gLkksnI~LNRKILAqLAI~DP~SFksLVd~~k~al~ 97 (184)
||||++|||+||+|||+|||||+|++|+|||+||+||+++||.|||||||||||.||.+|.+|++.++.+++
T Consensus 47 YrdRr~rKRdFR~LWI~RINAA~R~~GlsYS~fi~gLkkA~I~inRKvLadlAi~d~~aF~~lv~~aK~al~ 118 (118)
T COG0292 47 YRDRRQRKRDFRKLWIARINAAARENGLSYSRFINGLKKAGIEIDRKVLADLAINDPAAFAALVEKAKAALA 118 (118)
T ss_pred HHHHHHHhhHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHcCchhhHHHHHHHHhcCHHHHHHHHHHHHHhcC
Confidence 999999999999999999999999999999999999999999999999999999999999999999998763
No 2
>PTZ00030 60S ribosomal protein L20; Provisional
Probab=100.00 E-value=3.1e-33 Score=219.59 Aligned_cols=80 Identities=29% Similarity=0.402 Sum_probs=75.3
Q ss_pred chhhhhhh---------hchhhhhhhhhHHHHHHHHHhhhccCCCChHHHHHHHHHCCcccchhHHHHHHhcChhHHHHH
Q psy12837 18 PVWKTSKV---------CNEEINLTGHIGKLWTARITAGAEEHGVPYPLFREGLTRSNIMLDRKTLSDLAAWEPRTFKVK 88 (184)
Q Consensus 18 ~~w~~~k~---------yRDRKkKKRdFRrLWItRINAAaRe~GisYSkFI~gLkksnI~LNRKILAqLAI~DP~SFksL 88 (184)
+.+++|+. ||||++|||+||+|||+|||||+|++|++||.||++|+++||.||||||||||++||.+|++|
T Consensus 21 ~~~r~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~g~~Ys~fi~~L~k~~i~LNRK~Ls~LAi~dp~sF~~l 100 (121)
T PTZ00030 21 NCFKLARNRVMKALLYSYISRRKRKRILRVHWIQTINAATREHNMTYSRFINGLNNSNIQLNRKILANLAITEPFSFKAL 100 (121)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCCCcHHHHHHHHhcCHHHHHHH
Confidence 45666654 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHh
Q psy12837 89 KSTVGTTMC 97 (184)
Q Consensus 89 Vd~~k~al~ 97 (184)
++.++.++.
T Consensus 101 v~~~k~~l~ 109 (121)
T PTZ00030 101 VDESKYQLN 109 (121)
T ss_pred HHHHHHHhc
Confidence 999998765
No 3
>PRK05185 rplT 50S ribosomal protein L20; Provisional
Probab=99.98 E-value=5.6e-33 Score=215.81 Aligned_cols=76 Identities=32% Similarity=0.562 Sum_probs=72.2
Q ss_pred chhhhhhh---------hchhhhhhhhhHHHHHHHHHhhhccCCCChHHHHHHHHHCCcccchhHHHHHHhcChhHHHHH
Q psy12837 18 PVWKTSKV---------CNEEINLTGHIGKLWTARITAGAEEHGVPYPLFREGLTRSNIMLDRKTLSDLAAWEPRTFKVK 88 (184)
Q Consensus 18 ~~w~~~k~---------yRDRKkKKRdFRrLWItRINAAaRe~GisYSkFI~gLkksnI~LNRKILAqLAI~DP~SFksL 88 (184)
+.+++|+. ||||++|||+||+|||+|||||+|++|++||.||++|+++||.||||||||||++||.+|++|
T Consensus 29 ~~~r~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~g~~Ys~fi~~L~~~~i~LNRK~La~lAi~dp~~F~~l 108 (114)
T PRK05185 29 RLYRVAKQAVMKALQYAYRDRRQKKRDFRKLWIARINAAARQNGLSYSRFINGLKKAGIEIDRKVLADLAVNDPAAFAAL 108 (114)
T ss_pred cchHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhCCCccHHHHHHHHhcCHHHHHHH
Confidence 45666665 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHH
Q psy12837 89 KSTVG 93 (184)
Q Consensus 89 Vd~~k 93 (184)
++.++
T Consensus 109 v~~~k 113 (114)
T PRK05185 109 VEKAK 113 (114)
T ss_pred HHHHh
Confidence 99886
No 4
>TIGR01032 rplT_bact ribosomal protein L20. This protein binds directly to 23s ribosomal RNA and is necessary for the in vitro assembly process of the 50s ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. GO process changed accordingly
Probab=99.98 E-value=7.2e-33 Score=215.09 Aligned_cols=76 Identities=30% Similarity=0.535 Sum_probs=71.6
Q ss_pred chhhhhhh---------hchhhhhhhhhHHHHHHHHHhhhccCCCChHHHHHHHHHCCcccchhHHHHHHhcChhHHHHH
Q psy12837 18 PVWKTSKV---------CNEEINLTGHIGKLWTARITAGAEEHGVPYPLFREGLTRSNIMLDRKTLSDLAAWEPRTFKVK 88 (184)
Q Consensus 18 ~~w~~~k~---------yRDRKkKKRdFRrLWItRINAAaRe~GisYSkFI~gLkksnI~LNRKILAqLAI~DP~SFksL 88 (184)
+.+++|+. ||||++|||+||+|||+|||||+|++|++||.||++|+++||.||||||||||++||.+|++|
T Consensus 29 ~~~r~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~g~~Ys~fi~~L~~~~i~LnRKvLa~lAi~dp~~F~~l 108 (113)
T TIGR01032 29 RHYRVAKQTVIKAMAYAYRDRRQRKRDFRSLWITRINAAARQHGLSYSRFINGLKKANIEINRKVLSELAINDPEAFAEI 108 (113)
T ss_pred cchHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCCccHHHHHHHHhcCHHHHHHH
Confidence 45666665 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHH
Q psy12837 89 KSTVG 93 (184)
Q Consensus 89 Vd~~k 93 (184)
++.++
T Consensus 109 v~~~k 113 (113)
T TIGR01032 109 VEQAK 113 (113)
T ss_pred HHHhC
Confidence 99864
No 5
>CHL00068 rpl20 ribosomal protein L20
Probab=99.97 E-value=2.3e-32 Score=212.98 Aligned_cols=76 Identities=26% Similarity=0.516 Sum_probs=71.5
Q ss_pred chhhhhhh---------hchhhhhhhhhHHHHHHHHHhhhccCCCChHHHHHHHHHCCcccchhHHHHHHhcChhHHHHH
Q psy12837 18 PVWKTSKV---------CNEEINLTGHIGKLWTARITAGAEEHGVPYPLFREGLTRSNIMLDRKTLSDLAAWEPRTFKVK 88 (184)
Q Consensus 18 ~~w~~~k~---------yRDRKkKKRdFRrLWItRINAAaRe~GisYSkFI~gLkksnI~LNRKILAqLAI~DP~SFksL 88 (184)
+.+++|+. ||||++|||+||+|||+|||||+|++|++||.||++|+++||.||||||||||++||.+|++|
T Consensus 30 ~~~r~A~q~v~kAl~yayrdRk~kKR~fR~LWI~RINAa~R~~glsYs~fi~gL~~~~i~LnRKvLa~LAi~dp~~F~~l 109 (115)
T CHL00068 30 RLFRTANQQKMKALVSSYRDRKKKKRDFRRLWITRINAAIRENGVSYSKFIHNLYKNQILLNRKILAQIAILDPNCFYTI 109 (115)
T ss_pred ccHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCCccHHHHHHHHhcCHHHHHHH
Confidence 45666665 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHH
Q psy12837 89 KSTVG 93 (184)
Q Consensus 89 Vd~~k 93 (184)
++.+.
T Consensus 110 v~~~~ 114 (115)
T CHL00068 110 SNKII 114 (115)
T ss_pred HHHHh
Confidence 99764
No 6
>PRK14537 50S ribosomal protein L20/unknown domain fusion protein; Provisional
Probab=99.97 E-value=2.2e-31 Score=227.56 Aligned_cols=89 Identities=29% Similarity=0.446 Sum_probs=79.8
Q ss_pred chhhhhhh---------hchhhhhhhhhHHHHHHHHHhhhccCCCChHHHHHHHHHCCcccchhHHHHHHhcChhHHHHH
Q psy12837 18 PVWKTSKV---------CNEEINLTGHIGKLWTARITAGAEEHGVPYPLFREGLTRSNIMLDRKTLSDLAAWEPRTFKVK 88 (184)
Q Consensus 18 ~~w~~~k~---------yRDRKkKKRdFRrLWItRINAAaRe~GisYSkFI~gLkksnI~LNRKILAqLAI~DP~SFksL 88 (184)
+.+++|+. ||||++|||+||+|||+|||||+|++|++||.||++|+++||.||||||||||++||.+|.+|
T Consensus 30 ~lyR~A~q~V~KAL~YAYrdRK~KKRdFR~LWItRINAAaR~~GlsYS~fI~gLkka~I~LNRKvLAdLAI~Dp~sF~~L 109 (230)
T PRK14537 30 TLYKTAHEQVMRSLQYAYRDRKQRKRDFRKLWISRINAGAMLCGIKYSRLMHGLALAKVDINRKVLSDLAHLQPEVFVQY 109 (230)
T ss_pred cchHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCCccHHHHHHHHhcCHHHHHHH
Confidence 45666654 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhh-hhccccCC
Q psy12837 89 KSTVGTTMCR-IYQFYTKP 106 (184)
Q Consensus 89 Vd~~k~al~~-~~~~~~~p 106 (184)
++.++.++++ ..-|.++|
T Consensus 110 v~~ak~al~~~~~~~~~k~ 128 (230)
T PRK14537 110 VELAKKFLSQFQSTTITKP 128 (230)
T ss_pred HHHHHHHHHHHHHHhccCc
Confidence 9999998854 33345555
No 7
>PF00453 Ribosomal_L20: Ribosomal protein L20; InterPro: IPR005813 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 [, ]. L20 is a protein from the large (50S) subunit; in Escherichia coli it is known to bind directly to the 23S rRNA, and is required for ribosome assembly, but does not take part in protein synthesis. It belongs to a family of ribosomal proteins, including L20 from eubacteria, plant and alga chloroplasts and cyanelles [].; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBO_S 3CF5_N 3PIO_N 3PIP_N 2ZJQ_N 2ZJR_N 2ZJP_N 3DLL_N 3KIT_U 2X9U_U ....
Probab=99.97 E-value=1.8e-31 Score=205.42 Aligned_cols=71 Identities=37% Similarity=0.629 Sum_probs=67.6
Q ss_pred chhhhhhh---------hchhhhhhhhhHHHHHHHHHhhhccCCCChHHHHHHHHHCCcccchhHHHHHHhcChhHHHHH
Q psy12837 18 PVWKTSKV---------CNEEINLTGHIGKLWTARITAGAEEHGVPYPLFREGLTRSNIMLDRKTLSDLAAWEPRTFKVK 88 (184)
Q Consensus 18 ~~w~~~k~---------yRDRKkKKRdFRrLWItRINAAaRe~GisYSkFI~gLkksnI~LNRKILAqLAI~DP~SFksL 88 (184)
+.+++|+. |+||++|||+||+|||+|||||+|++|++||.||++|+++||.||||||||||++||.+|++|
T Consensus 29 ~~~r~a~q~v~kal~yay~~Rk~kKR~fR~lWI~RINAa~r~~g~~Ys~fi~~L~~~~i~LNRKiLa~LAi~dp~~F~~L 108 (108)
T PF00453_consen 29 NCYRIAKQQVMKALQYAYRDRKLKKRDFRRLWITRINAAAREHGLSYSRFINGLKKANIELNRKILADLAINDPESFKSL 108 (108)
T ss_dssp TSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSTHHHHHHHHHHCTSSTSCTTGGGHHTSSHHHHHHH
T ss_pred chHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHhCCcCcHHHHHHHHhcCHHHHhhC
Confidence 56677765 999999999999999999999999999999999999999999999999999999999999986
No 8
>KOG4707|consensus
Probab=99.85 E-value=3e-22 Score=162.43 Aligned_cols=72 Identities=38% Similarity=0.586 Sum_probs=69.8
Q ss_pred hhhhchhhhhhhhhHHHHHHHHHhhhccCCCChHHHHHHHHHCCcccchhHHHHHHhcChhHHHHHHHHHHH
Q psy12837 23 SKVCNEEINLTGHIGKLWTARITAGAEEHGVPYPLFREGLTRSNIMLDRKTLSDLAAWEPRTFKVKKSTVGT 94 (184)
Q Consensus 23 ~k~yRDRKkKKRdFRrLWItRINAAaRe~GisYSkFI~gLkksnI~LNRKILAqLAI~DP~SFksLVd~~k~ 94 (184)
++.++||++|||+||.|||+||||++++||+.||.|+++|.+++|.||||+|||||++||.||.+|++.+++
T Consensus 51 vy~~k~R~~kK~~mr~lwieRv~A~~~e~gv~y~~F~~~L~k~~ilLn~k~Lsqlai~eP~sf~~lv~~~k~ 122 (147)
T KOG4707|consen 51 VYATKDRYLKKRDMRTLWIERVNAGAAEHGVRYSPFKHGLHKSPILLNRKVLSQLAIVEPRSFCALVVLSKE 122 (147)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHhccccccccCCccccccchhHHHhhhhhhhCchhhhhHhhccHh
Confidence 345999999999999999999999999999999999999999999999999999999999999999999997
No 9
>KOG1255|consensus
Probab=91.43 E-value=0.11 Score=47.28 Aligned_cols=57 Identities=25% Similarity=0.369 Sum_probs=37.6
Q ss_pred hhhhhhhhhcccccc-eeeeeeCCCCcccccchhhccchhhhhhhhhcc---cccccccccccCchh
Q psy12837 109 HSCESQVQALDLYSM-KVKFHPLTGTQTCAPLFTRQTLSLTQIAAAKVI---DDEVVGSRHLEQPKY 171 (184)
Q Consensus 109 ~~~~~~~~a~dl~s~-kv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~ 171 (184)
..+..|..+|.++.. ||+||+|||+|+-- -+.|.+.. .-||+ ...--|..||-+|-+
T Consensus 24 s~y~~T~~nl~ink~TkVi~QGfTGKqgTF--Hs~q~~eY----gTk~VgG~~pkK~Gt~HLG~PVF 84 (329)
T KOG1255|consen 24 SLYNKTISNLKINKDTKVICQGFTGKQGTF--HSQQALEY----GTKVVGGVNPKKGGTTHLGLPVF 84 (329)
T ss_pred chhhhhhhceeecCCceEEEecccCCccce--eHHHHHHh----CCceeeccCCCcCcccccCchhh
Confidence 357788999999999 99999999999852 12222221 11221 223346789988865
No 10
>COG3514 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=59.24 E-value=3.7 Score=31.99 Aligned_cols=14 Identities=36% Similarity=0.582 Sum_probs=11.7
Q ss_pred HHHHHHHHhhhccC
Q psy12837 38 KLWTARITAGAEEH 51 (184)
Q Consensus 38 rLWItRINAAaRe~ 51 (184)
.=|-+|||++.|++
T Consensus 75 kGwQtRiN~aLR~~ 88 (93)
T COG3514 75 KGWQTRINAALRQY 88 (93)
T ss_pred ccHHHHHHHHHHHH
Confidence 34999999999964
No 11
>PTZ00187 succinyl-CoA synthetase alpha subunit; Provisional
Probab=55.80 E-value=4.8 Score=36.50 Aligned_cols=37 Identities=19% Similarity=0.190 Sum_probs=28.9
Q ss_pred chhhhhhhhhcccccc-eeeeeeCCCCcccccchhhccch
Q psy12837 108 YHSCESQVQALDLYSM-KVKFHPLTGTQTCAPLFTRQTLS 146 (184)
Q Consensus 108 ~~~~~~~~~a~dl~s~-kv~~~~~~~~~~~~~~~~~~~~~ 146 (184)
.+.++++.+++-++.+ ||.+|+|||+|+- ..|+|.+.
T Consensus 14 ~~~~~~~~~~i~~~~~t~v~vqGitg~~g~--~h~~~~~~ 51 (317)
T PTZ00187 14 RARSSTSAPRVWVNKNTKVICQGITGKQGT--FHTEQAIE 51 (317)
T ss_pred HHHHhccCccEEEcCCCeEEEecCCChHHH--HHHHHHHH
Confidence 3567788899888888 9999999999985 45555443
No 12
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=34.31 E-value=23 Score=23.22 Aligned_cols=21 Identities=33% Similarity=0.482 Sum_probs=15.3
Q ss_pred HHhhhccCCCChHHHHHHHHH
Q psy12837 44 ITAGAEEHGVPYPLFREGLTR 64 (184)
Q Consensus 44 INAAaRe~GisYSkFI~gLkk 64 (184)
|..||+.+|++++.+...++.
T Consensus 19 ~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 19 IRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHcC
Confidence 678999999999998766553
No 13
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=32.27 E-value=78 Score=21.68 Aligned_cols=55 Identities=9% Similarity=-0.027 Sum_probs=44.8
Q ss_pred HHHHHhhhccCCCChHHHHHHHHHCCcccchhHHHHHHhcChhHHHHHHHHHHHHHh
Q psy12837 41 TARITAGAEEHGVPYPLFREGLTRSNIMLDRKTLSDLAAWEPRTFKVKKSTVGTTMC 97 (184)
Q Consensus 41 ItRINAAaRe~GisYSkFI~gLkksnI~LNRKILAqLAI~DP~SFksLVd~~k~al~ 97 (184)
+.=|...|+.+|+|...-.+-|++.++ ++ -+...--+....++.-+++.+...|.
T Consensus 5 v~~Ie~~A~~~~~s~~ea~~~~~~~~~-~~-~i~~~Yd~lHt~s~~yivedi~~~l~ 59 (62)
T PF12668_consen 5 VFCIEEFAKKLNISGEEAYNYFKRSGV-ID-YIIDCYDVLHTQSDEYIVEDIIEYLK 59 (62)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHcCc-HH-HHHHcchHHHHCcHHHHHHHHHHHHH
Confidence 345889999999999999999999986 34 77777777888888888888776654
No 14
>PF11527 ARL2_Bind_BART: The ARF-like 2 binding protein BART; InterPro: IPR023379 This domain is found in ADP-ribosylation factor-like 2 (ARF2) binding protein, also known as BART, and in uncharacterised proteins. BART binds specifically to ARF2.GTP with a high affinity. However, it does not bind to ARF2.GDP. It is thought that this specific interaction is due to BART being the first identified ARF2-specific effector. The function is not completely characterised []. BART is predominantly cytosolic but can also be found to be associated with mitochondria. BART is also involved in binding to the adenine nucleotide transporter ANT1 []. ; PDB: 2K0S_A 2K9A_A 3DOF_B 3DOE_B.
Probab=28.95 E-value=1.2e+02 Score=23.15 Aligned_cols=60 Identities=18% Similarity=0.130 Sum_probs=50.2
Q ss_pred hhhHHHHHHHHHhhhccCCCChHHHHHHH---HHCCcccchhHHHHH-HhcChhHHHHHHHHHH
Q psy12837 34 GHIGKLWTARITAGAEEHGVPYPLFREGL---TRSNIMLDRKTLSDL-AAWEPRTFKVKKSTVG 93 (184)
Q Consensus 34 RdFRrLWItRINAAaRe~GisYSkFI~gL---kksnI~LNRKILAqL-AI~DP~SFksLVd~~k 93 (184)
+.|+.|--.-|...+.+.|++-..|...+ ....-.+.+.++.+| |..|-..|+.+.-.-+
T Consensus 51 ~ey~~lvE~~le~~l~~~g~s~e~f~~~~~~~~~~~~~~~~~i~e~Lla~~DF~~Fk~mM~~~n 114 (121)
T PF11527_consen 51 QEYKELVEKLLEEFLEELGISMEEFEEACLSEESQKDEIAGEIFEQLLAADDFEAFKEMMVQYN 114 (121)
T ss_dssp HHHHHHHHHHHHHHHHSTTSSHHCHHHHH---TCCCCCSSCCCHHHHCGGC-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHhhcccchhhhHHHHHHHHHHccHHHHHHHHHHHH
Confidence 35777888888888889999999999999 778888999999997 9999999999865433
No 15
>PF14384 DUF4415: Domain of unknown function (DUF4415)
Probab=27.50 E-value=29 Score=24.11 Aligned_cols=12 Identities=17% Similarity=0.351 Sum_probs=10.8
Q ss_pred HHHHHHhhhccC
Q psy12837 40 WTARITAGAEEH 51 (184)
Q Consensus 40 WItRINAAaRe~ 51 (184)
|-+|||++.|++
T Consensus 50 yQtriN~~Lr~~ 61 (62)
T PF14384_consen 50 YQTRINEALRKY 61 (62)
T ss_pred HHHHHHHHHHHh
Confidence 999999999864
No 16
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=25.97 E-value=69 Score=22.87 Aligned_cols=27 Identities=26% Similarity=0.230 Sum_probs=23.9
Q ss_pred HHhhhccCCCChHHHHHHHHHCCcccc
Q psy12837 44 ITAGAEEHGVPYPLFREGLTRSNIMLD 70 (184)
Q Consensus 44 INAAaRe~GisYSkFI~gLkksnI~LN 70 (184)
+..|++.-|++--.|+.-|++.||.+|
T Consensus 37 ~gkAAelag~s~~eF~~~L~~~gI~~~ 63 (76)
T PF03683_consen 37 LGKAAELAGMSRWEFLELLKERGIPIN 63 (76)
T ss_pred HHHHHHHhCCCHHHHHHHHHHCCCCCC
Confidence 356888899999999999999999866
No 17
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=25.70 E-value=65 Score=21.36 Aligned_cols=28 Identities=25% Similarity=0.304 Sum_probs=21.9
Q ss_pred HHHhhhccCCCChHHHHHHHHHCCcccc
Q psy12837 43 RITAGAEEHGVPYPLFREGLTRSNIMLD 70 (184)
Q Consensus 43 RINAAaRe~GisYSkFI~gLkksnI~LN 70 (184)
-|.+||+..|++++..-..|++..=.|+
T Consensus 15 s~~~AA~~l~is~~~vs~~i~~LE~~lg 42 (60)
T PF00126_consen 15 SISAAAEELGISQSAVSRQIKQLEEELG 42 (60)
T ss_dssp SHHHHHHHCTSSHHHHHHHHHHHHHHHT
T ss_pred CHHHHHHHhhccchHHHHHHHHHHHHhC
Confidence 4789999999999998888876544443
No 18
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=24.59 E-value=3.1e+02 Score=20.61 Aligned_cols=58 Identities=9% Similarity=0.111 Sum_probs=40.6
Q ss_pred hhHHHHHHHHHhhhccCCCChHHH--HHHHHHCCcccchhHHHHHHhcChhHHHHHHHHH
Q psy12837 35 HIGKLWTARITAGAEEHGVPYPLF--REGLTRSNIMLDRKTLSDLAAWEPRTFKVKKSTV 92 (184)
Q Consensus 35 dFRrLWItRINAAaRe~GisYSkF--I~gLkksnI~LNRKILAqLAI~DP~SFksLVd~~ 92 (184)
.+.+.|-..++...+.+|++.+.| +..|...+=.+.-.-||+.--.++.+...+++.-
T Consensus 11 ~~~~~~~~~~~~~l~~~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~L 70 (144)
T PRK03573 11 RLVRIWRALIDHRLKPLELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQL 70 (144)
T ss_pred HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHH
Confidence 356677778888999999998886 4555544333455677777777787777766643
No 19
>PRK13858 type IV secretion system T-DNA border endonuclease VirD1; Provisional
Probab=22.92 E-value=1.9e+02 Score=24.09 Aligned_cols=98 Identities=13% Similarity=0.101 Sum_probs=56.2
Q ss_pred chhhhhhhhchhhhhhhhh-------HHHHHHHHHhhhccCCCChHHHHHHHHHC---CcccchhHHHHH-HhcChhHHH
Q psy12837 18 PVWKTSKVCNEEINLTGHI-------GKLWTARITAGAEEHGVPYPLFREGLTRS---NIMLDRKTLSDL-AAWEPRTFK 86 (184)
Q Consensus 18 ~~w~~~k~yRDRKkKKRdF-------RrLWItRINAAaRe~GisYSkFI~gLkks---nI~LNRKILAqL-AI~DP~SFk 86 (184)
+.|.-+-+.|.|+-++..| ...=...|.+.|+..|+|=|.||..+-.. .|.++|.+..++ ++. ....
T Consensus 6 ~~~sd~~~~~~~~~~~~~~kvVsvRLTe~Ey~~L~~rA~~aGlS~SEfIRqAi~~~~g~V~v~r~T~e~~~~li--r~l~ 83 (147)
T PRK13858 6 GTSSDAAVDRRESAKVEGFKVVSTRLRSAEYESFSAQARLLGLSDSMAIRVAVRRIGGFLEIDAETREKMEAIL--QSIG 83 (147)
T ss_pred CCccccccccccCccccCCeEEEEecCHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCCeEeecccCHHHHHHHH--HHHH
Confidence 4444444444444444432 33445678999999999999999987754 455588666665 221 1222
Q ss_pred HHHHHHHHHHhhhhccccCCCchhhhhhhhhc
Q psy12837 87 VKKSTVGTTMCRIYQFYTKPSYHSCESQVQAL 118 (184)
Q Consensus 87 sLVd~~k~al~~~~~~~~~p~~~~~~~~~~a~ 118 (184)
.+..... +++...--...|.++.-+..++||
T Consensus 84 gianNLN-QLAr~aN~~~~~~~~~l~~er~~~ 114 (147)
T PRK13858 84 TLSSNIA-ALLSAYAENPRPDLEALRAERIAF 114 (147)
T ss_pred HHHHHHH-HHHHHHhcCCCCcHHHHHHHHHHH
Confidence 2222111 222222223336688888888886
No 20
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=22.01 E-value=61 Score=21.70 Aligned_cols=24 Identities=13% Similarity=0.085 Sum_probs=18.8
Q ss_pred HHHHhhhccCCCChHHHHHHHHHC
Q psy12837 42 ARITAGAEEHGVPYPLFREGLTRS 65 (184)
Q Consensus 42 tRINAAaRe~GisYSkFI~gLkks 65 (184)
..|+..|+++||+.+.|.+=+++.
T Consensus 24 ~sv~~va~~~gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 24 ESVSEVAREYGISPSTLYNWRKQY 47 (76)
T ss_dssp CHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CceEeeecccccccccccHHHHHH
Confidence 468899999999999887777665
No 21
>PF03050 DDE_Tnp_IS66: Transposase IS66 family ; InterPro: IPR004291 Transposase proteins are necessary for efficient DNA transposition. This family includes the bacterial insertion sequence (IS) element, IS66, from Agrobacterium tumefaciens []. IS66 may cause genetic and structural variations of the T region and the vir region of the octopine Ti plasmids []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=21.86 E-value=1e+02 Score=25.63 Aligned_cols=64 Identities=17% Similarity=0.210 Sum_probs=53.3
Q ss_pred cCCCChHHHHHHHHHCCcccchhHHHHHHhcChhHHHHHHHHHHHHHhhhhccccCCCchhhhhhhhhcc
Q psy12837 50 EHGVPYPLFREGLTRSNIMLDRKTLSDLAAWEPRTFKVKKSTVGTTMCRIYQFYTKPSYHSCESQVQALD 119 (184)
Q Consensus 50 e~GisYSkFI~gLkksnI~LNRKILAqLAI~DP~SFksLVd~~k~al~~~~~~~~~p~~~~~~~~~~a~d 119 (184)
.+++|+.+...-|...||.|.+.+|+++-..-...++.+.+.+++.+. ..|-+|.-|...+-+|
T Consensus 18 ~~~lp~~r~~~~~~~~G~~is~~ti~~~~~~~~~~l~~~~~~l~~~~~------~~~~~~~DET~~~vl~ 81 (271)
T PF03050_consen 18 VYHLPLYRIQQMLEDLGITISRGTIANWIKRVAEALKPLYEALKEELR------SSPVVHADETGWRVLD 81 (271)
T ss_pred cCCCCHHHHhhhhhccceeeccchhHhHhhhhhhhhhhhhhhhhhhcc------ccceeccCCceEEEec
Confidence 578999999999999999999999999998888888888888776553 4677777777777665
No 22
>PF15410 PH_9: Pleckstrin homology domain; PDB: 1WJM_A 1BTN_A 1MPH_A.
Probab=21.63 E-value=50 Score=24.99 Aligned_cols=11 Identities=27% Similarity=0.483 Sum_probs=8.5
Q ss_pred HHHHHHHHhhh
Q psy12837 38 KLWTARITAGA 48 (184)
Q Consensus 38 rLWItRINAAa 48 (184)
.-||.+||.+|
T Consensus 108 ~~Wi~~IN~~A 118 (119)
T PF15410_consen 108 NEWIDAINYAA 118 (119)
T ss_dssp HHHHHHHHHH-
T ss_pred HHHHHHHhhhc
Confidence 46999999876
No 23
>PRK01905 DNA-binding protein Fis; Provisional
Probab=21.27 E-value=80 Score=22.45 Aligned_cols=25 Identities=20% Similarity=0.278 Sum_probs=22.3
Q ss_pred HHHhhhccCCCChHHHHHHHHHCCc
Q psy12837 43 RITAGAEEHGVPYPLFREGLTRSNI 67 (184)
Q Consensus 43 RINAAaRe~GisYSkFI~gLkksnI 67 (184)
-+..+++..|++.+.+...|++.+|
T Consensus 52 n~s~aAr~LGIsrstL~rklkk~gi 76 (77)
T PRK01905 52 NQSLAAEYLGINRNTLRKKLQQHGL 76 (77)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHhCC
Confidence 3778999999999999999999876
No 24
>PF07818 HCNGP: HCNGP-like protein; InterPro: IPR012479 This family comprises sequences bearing significant similarity to the mouse transcriptional regulator protein HCNGP (Q02614 from SWISSPROT). This protein is localised to the nucleus and is thought to be involved in the regulation of beta-2-microglobulin genes.
Probab=21.23 E-value=1e+02 Score=23.51 Aligned_cols=38 Identities=16% Similarity=0.203 Sum_probs=31.2
Q ss_pred hHHHHHHHHHCCcccchhHHHHHHhcChhHHHHHHHHHH
Q psy12837 55 YPLFREGLTRSNIMLDRKTLSDLAAWEPRTFKVKKSTVG 93 (184)
Q Consensus 55 YSkFI~gLkksnI~LNRKILAqLAI~DP~SFksLVd~~k 93 (184)
..+| ..|++.|+.+|.++-+.-+..+|.-+..|++...
T Consensus 17 i~~f-l~lk~~G~~fN~~L~~s~~frNP~i~ekLi~~~~ 54 (96)
T PF07818_consen 17 IAKF-LELKRQGIHFNDRLQNSKSFRNPSILEKLIEFFG 54 (96)
T ss_pred HHHH-HHHHHcCCCHHHHHHHccccCChHHHHHHHHHcC
Confidence 4454 4566699999999999999999999999887653
No 25
>cd06093 PX_domain The Phox Homology domain, a phosphoinositide binding module. The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting.
Probab=20.54 E-value=58 Score=22.24 Aligned_cols=25 Identities=12% Similarity=0.142 Sum_probs=18.9
Q ss_pred ceeEEEEeeccccccchhhhhhhhchh
Q psy12837 3 SVRFHITTFHGKYYTPVWKTSKVCNEE 29 (184)
Q Consensus 3 ~~~~~~~~~~~~~~~~~w~~~k~yRDR 29 (184)
.+-|.|++..+. ...|.+.|+|.|=
T Consensus 17 ~~~Y~i~v~~~~--~~~~~v~rrysdF 41 (106)
T cd06093 17 YVVYIIEVTTQG--GEEWTVYRRYSDF 41 (106)
T ss_pred EEEEEEEEEECC--CCeEEEEeehHHH
Confidence 356777777766 6789999999763
No 26
>smart00216 VWD von Willebrand factor (vWF) type D domain. Von Willebrand factor contains several type D domains: D1 and D2 are present within the N-terminal propeptide whereas the remaining D domains are required for multimerisation.
Probab=20.03 E-value=42 Score=25.55 Aligned_cols=13 Identities=54% Similarity=0.593 Sum_probs=10.1
Q ss_pred EEEEeeccccccc
Q psy12837 6 FHITTFHGKYYTP 18 (184)
Q Consensus 6 ~~~~~~~~~~~~~ 18 (184)
-|++||.|+.|+-
T Consensus 18 ~~~~TFDg~~y~~ 30 (162)
T smart00216 18 PHYTTFDGVAYTF 30 (162)
T ss_pred CCeECcCCCEEee
Confidence 3889999988753
Done!