Query psy1551
Match_columns 190
No_of_seqs 192 out of 858
Neff 3.7
Searched_HMMs 46136
Date Fri Aug 16 23:08:48 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1551.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1551hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4021|consensus 100.0 3.3E-52 7.1E-57 354.3 7.3 129 60-188 58-186 (239)
2 TIGR00165 S18 ribosomal protei 100.0 3.9E-29 8.5E-34 181.6 6.9 66 109-175 4-69 (70)
3 PRK00391 rpsR 30S ribosomal pr 100.0 4.2E-29 9.1E-34 185.1 7.1 67 108-175 12-78 (79)
4 PRK13401 30S ribosomal protein 100.0 1.8E-28 4E-33 183.1 6.9 68 109-177 12-79 (82)
5 PRK13400 30S ribosomal protein 99.9 5.1E-27 1.1E-31 190.6 8.2 87 96-183 7-94 (147)
6 CHL00077 rps18 ribosomal prote 99.9 3.1E-26 6.6E-31 172.5 7.0 69 109-180 16-84 (86)
7 COG0238 RpsR Ribosomal protein 99.9 1.7E-25 3.7E-30 164.9 5.7 64 107-171 12-75 (75)
8 PF01084 Ribosomal_S18: Riboso 99.9 2.4E-23 5.2E-28 144.3 5.1 52 119-171 3-54 (54)
9 KOG3162|consensus 99.8 5.3E-19 1.1E-23 145.8 5.5 63 111-174 67-130 (159)
10 PF14354 Lar_restr_allev: Rest 65.7 3.1 6.8E-05 28.1 1.0 16 110-125 3-18 (61)
11 PRK09710 lar restriction allev 53.8 6.1 0.00013 28.9 0.8 27 110-138 6-32 (64)
12 TIGR03655 anti_R_Lar restricti 42.7 9.9 0.00021 25.6 0.4 13 111-123 2-14 (53)
13 PF09740 DUF2043: Uncharacteri 41.8 20 0.00043 28.6 2.0 19 5-23 2-20 (110)
14 PF00427 PBS_linker_poly: Phyc 37.9 20 0.00044 29.1 1.6 18 64-81 110-127 (131)
15 PF03470 zf-XS: XS zinc finger 33.6 31 0.00066 23.4 1.7 24 113-137 1-24 (43)
16 cd00630 RNAP_largest_subunit_C 31.7 15 0.00032 30.5 -0.1 30 121-151 79-108 (158)
17 PF14112 DUF4284: Domain of un 29.7 33 0.00072 26.9 1.6 74 112-189 31-105 (122)
18 COG1998 RPS31 Ribosomal protei 28.2 33 0.00071 24.2 1.1 26 102-127 10-36 (51)
19 KOG1403|consensus 27.7 20 0.00043 34.1 -0.0 13 69-81 305-317 (452)
20 TIGR02495 NrdG2 anaerobic ribo 22.9 93 0.002 24.7 3.0 62 109-170 26-91 (191)
21 PF13920 zf-C3HC4_3: Zinc fing 22.8 43 0.00094 21.7 0.9 13 109-121 36-48 (50)
22 KOG0878|consensus 22.0 42 0.00092 27.4 0.9 75 84-170 44-119 (124)
No 1
>KOG4021|consensus
Probab=100.00 E-value=3.3e-52 Score=354.28 Aligned_cols=129 Identities=47% Similarity=0.957 Sum_probs=125.1
Q ss_pred hhhHhhhccHHHHhhhCCCcccccccccCCCCCCCCCCCccccccceecCCCCCccccCCccccCcccHHHHhhcCCCCC
Q psy1551 60 EISIRYLASEAYQKCYGDEPVWKYYRRNHKGMFAPKKTRKTCIRSGIIATGNPCPICRDEYLIIHPYNIKLLEQFISPVN 139 (190)
Q Consensus 60 e~s~~Yl~S~~y~~~Yg~~pvw~~YRRNhKG~~pP~ktRktCir~gk~~~~npCpiCrd~~~~IDYKNV~LL~qFIs~~t 139 (190)
|+.|+||+|++|.++||+.|||.+|||||||+.+||+||+||||..++..+||||||||+++++||+|+.||+|||+++|
T Consensus 58 ~qp~kYlkS~~Y~e~Yg~~pVw~~YrRNhKG~~~pq~tRktCIrkn~~~~gnpCPICRDeyL~~DyRN~~LlEQF~~~ht 137 (239)
T KOG4021|consen 58 EQPSKYLKSRGYAEAYGGLPVWRWYRRNHKGQSKPQPTRKTCIRKNGRFLGNPCPICRDEYLYFDYRNPGLLEQFLADHT 137 (239)
T ss_pred hhHHHHHHHHHHHHHhcCCcHHHHHHhhccCCCCCCCchhHHHhhcCeecCCCCCccccceEEEeccCHHHHHHHhccCC
Confidence 36678999999999999999999999999999999999999999777778999999999999999999999999999999
Q ss_pred CeecccccccCCHHHHHHHHHHHHHHHHccccCcccCCcccccCCcCCC
Q psy1551 140 GEILSYMKTGVCQKQHLKLLVAITQAKNKGLITFDLPFREYNYKDYFPT 188 (190)
Q Consensus 140 GkILprr~TGlC~KqQRkL~kAIKrAR~lGLLPf~vpf~~ydy~~y~~~ 188 (190)
|+|+....||||.||+..|..||.+||++|+|.|.+||++|||++||++
T Consensus 138 g~~i~y~ktGlC~kqh~rL~~a~qkArdhG~lty~VpfR~~Dys~~yg~ 186 (239)
T KOG4021|consen 138 GQPIDYLKTGLCRKQHTRLRAALQKARDHGTLTYGVPFRNFDYSQWYGS 186 (239)
T ss_pred CCchhhhhcchHHHHHHHHHHHHHHhhhcCeEEecCCcccCchHHhccc
Confidence 9999999999999999999999999999999999999999999999986
No 2
>TIGR00165 S18 ribosomal protein S18. This ribosomal small subunit protein is found in all eubacteria so far, as well as in chloroplasts. YER050C from Saccharomyces cerevisiae and a related protein from Caenorhabditis elegans appear to be homologous and may represent mitochondrial forms. The trusted cutoff is set high enough that these two candidate S18 proteins are not categorized automatically.
Probab=99.96 E-value=3.9e-29 Score=181.64 Aligned_cols=66 Identities=27% Similarity=0.388 Sum_probs=62.9
Q ss_pred CCCCCccccCCccccCcccHHHHhhcCCCCCCeecccccccCCHHHHHHHHHHHHHHHHccccCccc
Q psy1551 109 TGNPCPICRDEYLIIHPYNIKLLEQFISPVNGEILSYMKTGVCQKQHLKLLVAITQAKNKGLITFDL 175 (190)
Q Consensus 109 ~~npCpiCrd~~~~IDYKNV~LL~qFIs~~tGkILprr~TGlC~KqQRkL~kAIKrAR~lGLLPf~v 175 (190)
.+++||||.+++..|||||++||++|||+ .|+|+||++||+|+||||+|++|||+||.+|||||+.
T Consensus 4 r~k~c~~~~~~~~~iDYKnv~lL~~Fis~-~GkIlpRriTgl~~k~Qr~l~~aIKrAR~~~LlP~~~ 69 (70)
T TIGR00165 4 RKKYCRFTAEGIQFIDYKDLDLLKKFISE-RGKILPRRITGTSAKYQRRLARAIKRARYLALLPYVK 69 (70)
T ss_pred CCCCCCccCCCCCcCCccCHHHHHHhcCC-CCeEcCCccCCcCHHHHHHHHHHHHHHHHHhcCCccC
Confidence 35789999999889999999999999999 5999999999999999999999999999999999985
No 3
>PRK00391 rpsR 30S ribosomal protein S18; Reviewed
Probab=99.96 E-value=4.2e-29 Score=185.10 Aligned_cols=67 Identities=28% Similarity=0.446 Sum_probs=63.9
Q ss_pred cCCCCCccccCCccccCcccHHHHhhcCCCCCCeecccccccCCHHHHHHHHHHHHHHHHccccCccc
Q psy1551 108 ATGNPCPICRDEYLIIHPYNIKLLEQFISPVNGEILSYMKTGVCQKQHLKLLVAITQAKNKGLITFDL 175 (190)
Q Consensus 108 ~~~npCpiCrd~~~~IDYKNV~LL~qFIs~~tGkILprr~TGlC~KqQRkL~kAIKrAR~lGLLPf~v 175 (190)
...++|+||.+++..|||||++||+||||+ +|+|+||++||+|+||||+|++|||+||.||||||+.
T Consensus 12 ~r~k~c~~c~~~~~~iDYKnv~lL~~Fis~-~GkIlprriTG~~~k~Qr~l~~aIkrAR~~~LlPf~~ 78 (79)
T PRK00391 12 RRKKVCRFCAEKIEYIDYKDVELLKKFISE-RGKILPRRITGTSAKHQRQLATAIKRARFLALLPYVD 78 (79)
T ss_pred CCCCCCcccCCCCCcCCccCHHHHHHhcCC-CceEcCcccCCcCHHHHHHHHHHHHHHHHhhCCCccC
Confidence 357799999999889999999999999999 6999999999999999999999999999999999985
No 4
>PRK13401 30S ribosomal protein S18; Provisional
Probab=99.95 E-value=1.8e-28 Score=183.11 Aligned_cols=68 Identities=22% Similarity=0.204 Sum_probs=65.0
Q ss_pred CCCCCccccCCccccCcccHHHHhhcCCCCCCeecccccccCCHHHHHHHHHHHHHHHHccccCcccCC
Q psy1551 109 TGNPCPICRDEYLIIHPYNIKLLEQFISPVNGEILSYMKTGVCQKQHLKLLVAITQAKNKGLITFDLPF 177 (190)
Q Consensus 109 ~~npCpiCrd~~~~IDYKNV~LL~qFIs~~tGkILprr~TGlC~KqQRkL~kAIKrAR~lGLLPf~vpf 177 (190)
.+++|+||.+++..|||||++||++|||+ +|+|+||++||||+||||+|++|||+||.||||||+...
T Consensus 12 r~k~c~~~~~~~~~iDYKnv~lL~~Fis~-~GkIlpRR~TGl~~k~QR~l~~AIKrAR~laLlPf~~~~ 79 (82)
T PRK13401 12 KAKKNLLDSLGIESVDYKDTALLRTFISD-RGKIRSRRVTGLTVQQQRQVATAIKNAREMALLPYPGRD 79 (82)
T ss_pred CCCCCCcccCCCCcCCccCHHHHHHhcCC-CccCcCcccCCcCHHHHHHHHHHHHHHHHHhcCccccCC
Confidence 57899999999999999999999999999 699999999999999999999999999999999998765
No 5
>PRK13400 30S ribosomal protein S18; Provisional
Probab=99.94 E-value=5.1e-27 Score=190.56 Aligned_cols=87 Identities=22% Similarity=0.293 Sum_probs=73.6
Q ss_pred CCCcccccccee-cCCCCCccccCCccccCcccHHHHhhcCCCCCCeecccccccCCHHHHHHHHHHHHHHHHccccCcc
Q psy1551 96 KTRKTCIRSGII-ATGNPCPICRDEYLIIHPYNIKLLEQFISPVNGEILSYMKTGVCQKQHLKLLVAITQAKNKGLITFD 174 (190)
Q Consensus 96 ktRktCir~gk~-~~~npCpiCrd~~~~IDYKNV~LL~qFIs~~tGkILprr~TGlC~KqQRkL~kAIKrAR~lGLLPf~ 174 (190)
-||..-...+++ ..++.|+||.+++..|||||++||++|||+ +|||+|||+||+|+||||+|++|||+||.||||||+
T Consensus 7 ~~r~~~~gr~~~~~RrK~C~~c~~~~~~IDYKNv~lL~~FISe-~GKIlPRRiTGlcaK~QRkLakAIKRAR~laLLPfv 85 (147)
T PRK13400 7 PNRPARGGRGRYTPKRKICSFCAEKVSRIDYKDSAKLARYISD-RGKIEPRRRTGTCARHQRALANAIKRARFIALMPFV 85 (147)
T ss_pred CCCcCcCCCCccCCCCCCCCccCCCCCccCCcCHHHHHHhcCc-CccCcCcccCCcCHHHHHHHHHHHHHHHHHhccccc
Confidence 344433323333 356789999999999999999999999999 699999999999999999999999999999999999
Q ss_pred cCCcccccC
Q psy1551 175 LPFREYNYK 183 (190)
Q Consensus 175 vpf~~ydy~ 183 (190)
..+....-+
T Consensus 86 ~~~ir~~g~ 94 (147)
T PRK13400 86 SEHVRRQGN 94 (147)
T ss_pred cccccccCC
Confidence 988766543
No 6
>CHL00077 rps18 ribosomal protein S18
Probab=99.93 E-value=3.1e-26 Score=172.49 Aligned_cols=69 Identities=32% Similarity=0.339 Sum_probs=63.8
Q ss_pred CCCCCccccCCccccCcccHHHHhhcCCCCCCeecccccccCCHHHHHHHHHHHHHHHHccccCcccCCccc
Q psy1551 109 TGNPCPICRDEYLIIHPYNIKLLEQFISPVNGEILSYMKTGVCQKQHLKLLVAITQAKNKGLITFDLPFREY 180 (190)
Q Consensus 109 ~~npCpiCrd~~~~IDYKNV~LL~qFIs~~tGkILprr~TGlC~KqQRkL~kAIKrAR~lGLLPf~vpf~~y 180 (190)
..+.||||... .|||||++||++|||+ +|+|+||++||||+||||+|++|||+||.+|||||+.....|
T Consensus 16 rrk~~~~~~~~--~iDYKnv~lL~~Fis~-~GkIlpRriTGl~~K~QR~l~~aIKrAR~~gLlP~~~~~~~f 84 (86)
T CHL00077 16 RRRLPPIQSGD--RIDYKNMSLLSRFISE-QGKILSRRVTRLTLKQQRLITKAIKQARILSLLPFLNNEKQF 84 (86)
T ss_pred ccCCCCCCCCC--cCCccCHHHHHHhcCC-CCeEcCcccCCcCHHHHHHHHHHHHHHHHHhcCCcccccccc
Confidence 46789999875 6999999999999999 699999999999999999999999999999999999876554
No 7
>COG0238 RpsR Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=1.7e-25 Score=164.86 Aligned_cols=64 Identities=28% Similarity=0.403 Sum_probs=60.9
Q ss_pred ecCCCCCccccCCccccCcccHHHHhhcCCCCCCeecccccccCCHHHHHHHHHHHHHHHHcccc
Q psy1551 107 IATGNPCPICRDEYLIIHPYNIKLLEQFISPVNGEILSYMKTGVCQKQHLKLLVAITQAKNKGLI 171 (190)
Q Consensus 107 ~~~~npCpiCrd~~~~IDYKNV~LL~qFIs~~tGkILprr~TGlC~KqQRkL~kAIKrAR~lGLL 171 (190)
....+.|+||..++..|||||+++|++|||+ +|||+||++||+|+|+||+|+.||||||.+|||
T Consensus 12 ~rrrk~c~~~~~~~~~iDYKd~~~L~rfise-~GKI~prRiTG~sak~QR~la~AIKRAR~laLl 75 (75)
T COG0238 12 FRRRKVCRFTAEGIEEIDYKDVELLKRFISE-RGKILPRRITGTSAKHQRRLARAIKRARYLALL 75 (75)
T ss_pred cccccccccccccCCccCccCHHHHHHHhcc-cCcccccccccccHHHHHHHHHHHHHHHHHhcC
Confidence 3467899999998899999999999999999 799999999999999999999999999999997
No 8
>PF01084 Ribosomal_S18: Ribosomal protein S18; InterPro: IPR001648 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 [, ]. 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 S18 is known to be involved in binding the aminoacyl-tRNA complex in Escherichia coli [], and appears to be situated at the tRNA A-site. Experimental evidence has revealed that S18 is well exposed on the surface of the E. coli ribosome, and is a secondary rRNA binding protein []. S18 belongs to a family of ribosomal proteins [] that includes: eubacterial S18; metazoan mitochondrial S18, algal and plant chloroplast S18; and cyanelle S18.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2UXD_R 3I8G_U 3UZ7_U 1N33_R 2XSY_R 3V24_R 3OGY_R 2XUY_R 2XFZ_R 3UXT_R ....
Probab=99.88 E-value=2.4e-23 Score=144.31 Aligned_cols=52 Identities=46% Similarity=0.658 Sum_probs=49.9
Q ss_pred CccccCcccHHHHhhcCCCCCCeecccccccCCHHHHHHHHHHHHHHHHcccc
Q psy1551 119 EYLIIHPYNIKLLEQFISPVNGEILSYMKTGVCQKQHLKLLVAITQAKNKGLI 171 (190)
Q Consensus 119 ~~~~IDYKNV~LL~qFIs~~tGkILprr~TGlC~KqQRkL~kAIKrAR~lGLL 171 (190)
+...|||||+.||+|||++ +|+|+||++||||+||||+|++|||+||++|||
T Consensus 3 ~~~~idykn~~lL~~Fi~~-~GkIl~rr~Tgl~~k~Qr~l~~aIkrAR~~gLl 54 (54)
T PF01084_consen 3 NNEYIDYKNVELLSQFISP-TGKILPRRITGLCAKQQRKLAKAIKRARQLGLL 54 (54)
T ss_dssp SSSSSSSSSHHHHGCGBTT-SSSBSTHHHHTSTHHHHHHHHHHHHHHHHTTSS
T ss_pred CCCcCCcCCHHHHHHHcCc-ccceehhhhccccHHHHHHHHHHHHHHHHhhCC
Confidence 4478999999999999999 799999999999999999999999999999997
No 9
>KOG3162|consensus
Probab=99.76 E-value=5.3e-19 Score=145.77 Aligned_cols=63 Identities=33% Similarity=0.516 Sum_probs=56.8
Q ss_pred CCCccccCCcc-ccCcccHHHHhhcCCCCCCeecccccccCCHHHHHHHHHHHHHHHHccccCcc
Q psy1551 111 NPCPICRDEYL-IIHPYNIKLLEQFISPVNGEILSYMKTGVCQKQHLKLLVAITQAKNKGLITFD 174 (190)
Q Consensus 111 npCpiCrd~~~-~IDYKNV~LL~qFIs~~tGkILprr~TGlC~KqQRkL~kAIKrAR~lGLLPf~ 174 (190)
..|++|..++. .++||||.||+|||+++ |.||||++||||+|+||+|.+||++||.+||||+.
T Consensus 67 ~~c~~c~~~Vd~~~~yknv~iLsqFv~~~-G~il~RkiTGLc~k~Qrki~~aI~~A~~~GlmP~~ 130 (159)
T KOG3162|consen 67 PQCILCTKGVDIKLSYKNVLLLSQFVSED-GGILPRKITGLCAKNQRKIERAIKRARAAGLMPVT 130 (159)
T ss_pred ccCcccccCCCcccccCccchhhhhcccc-cceecchhhhhhHHHHHHHHHHHHHHHHhcccccc
Confidence 56999998842 34599999999999997 77999999999999999999999999999999944
No 10
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=65.69 E-value=3.1 Score=28.09 Aligned_cols=16 Identities=31% Similarity=0.860 Sum_probs=10.3
Q ss_pred CCCCccccCCccccCc
Q psy1551 110 GNPCPICRDEYLIIHP 125 (190)
Q Consensus 110 ~npCpiCrd~~~~IDY 125 (190)
=+|||||....+.+++
T Consensus 3 LkPCPFCG~~~~~~~~ 18 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQ 18 (61)
T ss_pred CcCCCCCCCcceEeec
Confidence 3699999655444443
No 11
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=53.81 E-value=6.1 Score=28.87 Aligned_cols=27 Identities=15% Similarity=0.256 Sum_probs=16.2
Q ss_pred CCCCccccCCccccCcccHHHHhhcCCCC
Q psy1551 110 GNPCPICRDEYLIIHPYNIKLLEQFISPV 138 (190)
Q Consensus 110 ~npCpiCrd~~~~IDYKNV~LL~qFIs~~ 138 (190)
-+|||||..+.+.+... ..--+|++..
T Consensus 6 lKPCPFCG~~~~~v~~~--~g~~~v~C~~ 32 (64)
T PRK09710 6 VKPCPFCGCPSVTVKAI--SGYYRAKCNG 32 (64)
T ss_pred ccCCCCCCCceeEEEec--CceEEEEcCC
Confidence 47999999885544432 2233455553
No 12
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=42.68 E-value=9.9 Score=25.62 Aligned_cols=13 Identities=31% Similarity=1.030 Sum_probs=9.3
Q ss_pred CCCccccCCcccc
Q psy1551 111 NPCPICRDEYLII 123 (190)
Q Consensus 111 npCpiCrd~~~~I 123 (190)
+|||||...-..+
T Consensus 2 kPCPfCGg~~~~~ 14 (53)
T TIGR03655 2 KPCPFCGGADVYL 14 (53)
T ss_pred CCCCCCCCcceee
Confidence 6999998764434
No 13
>PF09740 DUF2043: Uncharacterized conserved protein (DUF2043); InterPro: IPR018610 This entry consists of uncharacterised proteins of unknown function. They contain three conserved cysteines and a {CP}{y/l}{HG} motif.
Probab=41.77 E-value=20 Score=28.61 Aligned_cols=19 Identities=32% Similarity=0.384 Sum_probs=13.2
Q ss_pred ccCCCccCCccceeecCCc
Q psy1551 5 ETAPVIPESEVWDVWIPPQ 23 (190)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~ 23 (190)
..|||+|-.-.-+.|=--+
T Consensus 2 ~~APvvp~g~dL~yWG~~~ 20 (110)
T PF09740_consen 2 ARAPVVPFGLDLYYWGQEQ 20 (110)
T ss_pred CCCCEecccchhccccccc
Confidence 3588888887777775433
No 14
>PF00427 PBS_linker_poly: Phycobilisome Linker polypeptide; InterPro: IPR001297 Phycobilisomes (PBSs) are the major light-harvesting systems in cyanobacteria and red algae. PBS is a supercomplex that is composed of a core complex and multiple peripheral rod complexes. Typically, the core consists of two or five cylinders lying on the membrane with, in most cases, multiple rods radiating from the core to form a hemidiscoidal structure. The building units of the core cylinders and the peripheral rods are trimeric and hexameric discs, in which a monomer consists of a pair of related phycobiliproteins (PBPs), such as phycorerythrins, phycoerythrocyanins, phycocyanins, and allophycocyanins. The discs are connected to each other via specific linker polypeptides to form peripheral rods or core cylinders. Linker polypeptides share a conserved domain of ~180 residues, which can be present in one or multiple copies [, , , , ].; GO: 0015979 photosynthesis, 0030089 phycobilisome; PDB: 2L8V_A 2KY4_A 3OSJ_D 2L06_A 3NPH_B 2L3W_A 3PRU_C 3OHW_A.
Probab=37.88 E-value=20 Score=29.13 Aligned_cols=18 Identities=33% Similarity=0.600 Sum_probs=15.3
Q ss_pred hhhccHHHHhhhCCCccc
Q psy1551 64 RYLASEAYQKCYGDEPVW 81 (190)
Q Consensus 64 ~Yl~S~~y~~~Yg~~pvw 81 (190)
.+++|++|.+.+|++-|-
T Consensus 110 ~lldS~EY~~~FG~d~VP 127 (131)
T PF00427_consen 110 ALLDSEEYLEAFGEDTVP 127 (131)
T ss_dssp HHHTSHHHHHHTTTTBE-
T ss_pred HHHCcHHHHHHcCCCCCC
Confidence 489999999999998764
No 15
>PF03470 zf-XS: XS zinc finger domain; InterPro: IPR005381 This domain is a putative nucleic acid binding zinc finger and is found at the N terminus of proteins that also contain an adjacent XS domain IPR005380 from INTERPRO and in some proteins a C-terminal XH domain IPR005379 from INTERPRO.
Probab=33.63 E-value=31 Score=23.44 Aligned_cols=24 Identities=21% Similarity=0.333 Sum_probs=17.6
Q ss_pred CccccCCccccCcccHHHHhhcCCC
Q psy1551 113 CPICRDEYLIIHPYNIKLLEQFISP 137 (190)
Q Consensus 113 CpiCrd~~~~IDYKNV~LL~qFIs~ 137 (190)
||||..+. .=||+=-+||+.=..-
T Consensus 1 CP~C~~kk-k~~Y~~~~LlqHA~gv 24 (43)
T PF03470_consen 1 CPFCPGKK-KQDYKYRELLQHASGV 24 (43)
T ss_pred CCCCCCCC-CcceehhHHHHHHHhh
Confidence 99999873 4558877788765544
No 16
>cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain. RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channe
Probab=31.70 E-value=15 Score=30.49 Aligned_cols=30 Identities=13% Similarity=0.341 Sum_probs=28.0
Q ss_pred cccCcccHHHHhhcCCCCCCeecccccccCC
Q psy1551 121 LIIHPYNIKLLEQFISPVNGEILSYMKTGVC 151 (190)
Q Consensus 121 ~~IDYKNV~LL~qFIs~~tGkILprr~TGlC 151 (190)
..||+|.+.||..+|+- +|.+++-.+.|+.
T Consensus 79 i~V~~rHl~LIAD~MT~-~G~~~ginr~g~~ 108 (158)
T cd00630 79 VSVDRRHIELIADVMTY-SGGLRGVTRSGFR 108 (158)
T ss_pred ceecHHHHHHHHHHHhc-CCccccccccccc
Confidence 67999999999999999 7999999999985
No 17
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=29.70 E-value=33 Score=26.88 Aligned_cols=74 Identities=19% Similarity=0.275 Sum_probs=54.5
Q ss_pred CCccccCCccccCcccHHHHhhcCCCCCCe-ecccccccCCHHHHHHHHHHHHHHHHccccCcccCCcccccCCcCCCC
Q psy1551 112 PCPICRDEYLIIHPYNIKLLEQFISPVNGE-ILSYMKTGVCQKQHLKLLVAITQAKNKGLITFDLPFREYNYKDYFPTS 189 (190)
Q Consensus 112 pCpiCrd~~~~IDYKNV~LL~qFIs~~tGk-ILprr~TGlC~KqQRkL~kAIKrAR~lGLLPf~vpf~~ydy~~y~~~~ 189 (190)
+|.||++- .|||-|-+++..-..+. .. =+..-..|.+-.. ..|.+.++.+...+.-++..=+.-|++...|+.+
T Consensus 31 ~s~F~~df--~i~~yDeDfie~~~~~~-~~~~l~~ll~~~Sy~~-~~i~~~~~~~~~~~~~~~Naii~~yn~~~~y~~~ 105 (122)
T PF14112_consen 31 PSQFCKDF--GIDYYDEDFIEIIFYEE-SEVSLEELLEGFSYDE-SIIPKIKEKCKEKLIKKYNAIILYYNFEIIYDES 105 (122)
T ss_pred cChHHHHc--CCCccCchhcEEEEccC-CccCHHHHHhcCCccH-HHHHHHHHHHHhhcCCCccEEEEEECCcccCCcc
Confidence 89999986 57766999888777773 33 4455567777655 5588888888888888888888888888666554
No 18
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=28.24 E-value=33 Score=24.18 Aligned_cols=26 Identities=12% Similarity=0.358 Sum_probs=18.0
Q ss_pred cccceec-CCCCCccccCCccccCccc
Q psy1551 102 IRSGIIA-TGNPCPICRDEYLIIHPYN 127 (190)
Q Consensus 102 ir~gk~~-~~npCpiCrd~~~~IDYKN 127 (190)
+.++++. .++-||-|..+..--||+|
T Consensus 10 v~~~kv~rk~~~CPrCG~gvfmA~H~d 36 (51)
T COG1998 10 VDDEKVKRKNRFCPRCGPGVFMADHKD 36 (51)
T ss_pred EcCCcEEEccccCCCCCCcchhhhcCc
Confidence 4555655 3556999998876667766
No 19
>KOG1403|consensus
Probab=27.71 E-value=20 Score=34.14 Aligned_cols=13 Identities=38% Similarity=0.685 Sum_probs=11.1
Q ss_pred HHHHhhhCCCccc
Q psy1551 69 EAYQKCYGDEPVW 81 (190)
Q Consensus 69 ~~y~~~Yg~~pvw 81 (190)
-+|.+||||+||-
T Consensus 305 v~YFNTyGGnPVs 317 (452)
T KOG1403|consen 305 VEYFNTYGGNPVS 317 (452)
T ss_pred ceehhccCCCchh
Confidence 3689999999985
No 20
>TIGR02495 NrdG2 anaerobic ribonucleoside-triphosphate reductase activating protein. This enzyme is a member of the radical-SAM family (pfam04055). It is often gene clustered with the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, TIGR02487) and presumably fulfills the identical function as NrdG which utilizes S-adenosyl methionine, an iron-sulfur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centered radical in NrdD.
Probab=22.85 E-value=93 Score=24.70 Aligned_cols=62 Identities=19% Similarity=0.287 Sum_probs=41.5
Q ss_pred CCCCCccccCCcc----ccCcccHHHHhhcCCCCCCeecccccccCCHHHHHHHHHHHHHHHHccc
Q psy1551 109 TGNPCPICRDEYL----IIHPYNIKLLEQFISPVNGEILSYMKTGVCQKQHLKLLVAITQAKNKGL 170 (190)
Q Consensus 109 ~~npCpiCrd~~~----~IDYKNV~LL~qFIs~~tGkILprr~TGlC~KqQRkL~kAIKrAR~lGL 170 (190)
|+--|++|-.... .-.+.+++.+..+|....+.+.-=..||=-+--+..+...|+.++..|+
T Consensus 26 Cnl~C~~C~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~i~~sGGEPll~~~l~~li~~~~~~g~ 91 (191)
T TIGR02495 26 CNLKCPYCHNPELIDREGSGEIEVEFLLEFLRSRQGLIDGVVITGGEPTLQAGLPDFLRKVRELGF 91 (191)
T ss_pred CCCCCCCCCCccccCCCCCCcCCHHHHHHHHHHhcCCCCeEEEECCcccCcHhHHHHHHHHHHCCC
Confidence 7788999976421 1235677777777777433333335788666666668888899988885
No 21
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=22.83 E-value=43 Score=21.66 Aligned_cols=13 Identities=38% Similarity=0.899 Sum_probs=9.7
Q ss_pred CCCCCccccCCcc
Q psy1551 109 TGNPCPICRDEYL 121 (190)
Q Consensus 109 ~~npCpiCrd~~~ 121 (190)
.++.||+|+..+.
T Consensus 36 ~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 36 RKKKCPICRQPIE 48 (50)
T ss_dssp TTSBBTTTTBB-S
T ss_pred cCCCCCcCChhhc
Confidence 4778999998754
No 22
>KOG0878|consensus
Probab=22.04 E-value=42 Score=27.40 Aligned_cols=75 Identities=21% Similarity=0.262 Sum_probs=43.0
Q ss_pred ccccCCCCC-CCCCCCccccccceecCCCCCccccCCccccCcccHHHHhhcCCCCCCeecccccccCCHHHHHHHHHHH
Q psy1551 84 YRRNHKGMF-APKKTRKTCIRSGIIATGNPCPICRDEYLIIHPYNIKLLEQFISPVNGEILSYMKTGVCQKQHLKLLVAI 162 (190)
Q Consensus 84 YRRNhKG~~-pP~ktRktCir~gk~~~~npCpiCrd~~~~IDYKNV~LL~qFIs~~tGkILprr~TGlC~KqQRkL~kAI 162 (190)
-||.+||++ .|.- .....|. ++..||---.+.+.-+-++.++|-----.+-|+| .-+++++....| +
T Consensus 44 VrRRFkgqilMPnI----gYgsnKk-Trh~lP~G~~kflv~nvkele~Llm~nk~YcaEI----AhnVsak~r~~I---v 111 (124)
T KOG0878|consen 44 VRRRFKGQILMPNI----GYGSNKK-TRHMLPNGFKKFLVHNVKELEVLLMHNKTYCAEI----AHNVSAKKRKAI---V 111 (124)
T ss_pred HHHHhccceecccc----ccCCCcc-ceecCChhhhHHhhhhhhHHHHHHHhhHHHHHHH----hhccccccHHHH---H
Confidence 468899996 4420 0111222 3445554444444444566666654444445666 568888887766 6
Q ss_pred HHHHHccc
Q psy1551 163 TQAKNKGL 170 (190)
Q Consensus 163 KrAR~lGL 170 (190)
.+|.++|+
T Consensus 112 era~qL~i 119 (124)
T KOG0878|consen 112 ERAAQLGI 119 (124)
T ss_pred HHHHhhce
Confidence 78888874
Done!