Query 033009
Match_columns 129
No_of_seqs 111 out of 1032
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 08:40:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033009.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033009hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00158 40S ribosomal protein 100.0 1.7E-50 3.8E-55 290.6 14.2 129 1-129 1-130 (130)
2 PLN00146 40S ribosomal protein 100.0 2.5E-50 5.5E-55 290.1 14.1 129 1-129 1-130 (130)
3 COG0096 RpsH Ribosomal protein 100.0 2.1E-50 4.6E-55 289.7 12.6 122 1-129 1-132 (132)
4 PRK04034 rps8p 30S ribosomal p 100.0 1.4E-48 3.1E-53 281.0 13.9 128 1-129 1-130 (130)
5 CHL00042 rps8 ribosomal protei 100.0 4.3E-47 9.4E-52 273.9 13.0 122 1-129 1-132 (132)
6 PRK00136 rpsH 30S ribosomal pr 100.0 1.7E-45 3.7E-50 264.9 13.3 121 1-129 1-130 (130)
7 PF00410 Ribosomal_S8: Ribosom 100.0 2.9E-44 6.4E-49 257.9 11.5 119 4-129 1-129 (129)
8 KOG1754 40S ribosomal protein 100.0 2.5E-40 5.4E-45 233.8 11.2 129 1-129 1-130 (130)
9 PF09639 YjcQ: YjcQ protein; 55.1 5.6 0.00012 26.4 0.7 24 31-54 25-48 (88)
10 COG2519 GCD14 tRNA(1-methylade 49.9 29 0.00063 27.8 4.1 43 5-47 173-215 (256)
11 PF08438 MMR_HSR1_C: GTPase of 48.0 30 0.00064 24.2 3.5 37 7-47 11-47 (109)
12 PF10264 Stork_head: Winged he 47.6 9 0.0002 25.4 0.8 36 10-46 32-67 (80)
13 PF09879 DUF2106: Predicted me 43.2 11 0.00024 27.8 0.8 17 96-112 105-121 (153)
14 PF13732 DUF4162: Domain of un 38.7 44 0.00095 21.0 3.0 32 22-54 43-74 (84)
15 PHA02943 hypothetical protein; 36.5 44 0.00096 25.0 3.1 24 29-52 37-60 (165)
16 COG1244 Predicted Fe-S oxidore 36.5 44 0.00096 28.0 3.4 41 4-45 221-261 (358)
17 PHA02745 hypothetical protein; 33.5 28 0.00061 27.8 1.7 47 43-89 120-170 (265)
18 PF02813 Retro_M: Retroviral M 29.2 41 0.00089 22.4 1.7 22 28-49 20-41 (86)
19 COG1591 Holliday junction reso 27.1 1.2E+02 0.0027 22.1 4.0 56 29-90 6-73 (137)
20 COG4037 Predicted membrane pro 26.1 32 0.00069 25.2 0.8 18 96-113 109-126 (163)
21 PF09572 RE_XamI: XamI restric 23.7 73 0.0016 25.5 2.5 32 5-47 103-140 (251)
22 PF02618 YceG: YceG-like famil 22.3 1.3E+02 0.0027 24.2 3.7 44 5-50 55-98 (297)
23 PF13601 HTH_34: Winged helix 22.0 1.2E+02 0.0026 19.5 2.9 24 28-52 27-50 (80)
24 PRK15453 phosphoribulokinase; 21.8 1E+02 0.0023 25.1 3.1 33 7-40 243-275 (290)
25 cd02029 PRK_like Phosphoribulo 21.1 1.1E+02 0.0024 24.9 3.0 34 6-40 236-269 (277)
26 TIGR03433 padR_acidobact trans 20.8 1.6E+02 0.0034 19.5 3.4 41 7-52 21-61 (100)
27 PF08643 DUF1776: Fungal famil 20.1 84 0.0018 25.7 2.2 33 19-51 1-35 (299)
No 1
>PTZ00158 40S ribosomal protein S15A; Provisional
Probab=100.00 E-value=1.7e-50 Score=290.60 Aligned_cols=129 Identities=48% Similarity=0.809 Sum_probs=123.8
Q ss_pred CC-CcHHHHHHHHhhhhhhcCCCeEEEecChhHHHHHHHhhccCCcccceEEEcCCCcceEEEEEccccCCCCcccccee
Q 033009 1 MG-RRILNDALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYIKDFQLYDPHRVGKIKVELLGRVNDCRGLTYRQD 79 (129)
Q Consensus 1 M~-~d~iad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eG~I~~~~~~~~~~~~~i~I~Lky~~~k~~~IspRvy 79 (129)
|+ +||+|||||+||||++++|++|.++|+||++.+||++|++||||++|++.+++....+.+.|+.+.++++.||||+|
T Consensus 1 m~~~~~iadmlt~IrNa~~~~~~~V~v~p~Skl~~~il~IL~~eGyI~~~~~~~~~~~~~i~v~l~~rIsk~g~IS~RvY 80 (130)
T PTZ00158 1 MVRMSVLADCLRSIVNAEKQGKRQVLIRPSSKVVVKFLQVMQKHGYIGEFEIVDDHRSGKIVVNLNGRLNKCGVISPRFD 80 (130)
T ss_pred CCcccHHHHHHHhhhhHHhCCCCeEEEeCCcHHHHHHHHHHHHCCcccceEEEecCCEEEEEEEEcCccccCCCCccceE
Confidence 77 49999999999999999999999569999999999999999999999987776677889999999999999999999
Q ss_pred ccccchhhhhcccCCCCcceEEEEECCCCcccHHHHHhcCCCeEEEEEEC
Q 033009 80 VKAREIEGYTVHALPTRQWGYVVITTPDGVLDHEEALRRNVGGQVLGYFH 129 (129)
Q Consensus 80 ~~~~~l~~~~~~~~p~~~~Gi~IlSTskGimt~~eA~~~~vGGevL~~v~ 129 (129)
+++++||++.+||+|.+|+|++|||||+|||||+||+++++|||+||+||
T Consensus 81 ~~~~~ip~v~~~~lp~~glGi~IlSTSkGImt~~eAr~~~vGGEvLc~v~ 130 (130)
T PTZ00158 81 VTLGEFEKWANNILPSRQFGHVVLTTSYGIMDHEEARRRHTGGKILGFFY 130 (130)
T ss_pred CCcchhhHHhcCCCccccceEEEEECCCCccChHHHHHcCCCceEEEEEC
Confidence 99999999999999999999999999999999999999999999999998
No 2
>PLN00146 40S ribosomal protein S15a; Provisional
Probab=100.00 E-value=2.5e-50 Score=290.13 Aligned_cols=129 Identities=53% Similarity=0.914 Sum_probs=122.6
Q ss_pred CCC-cHHHHHHHHhhhhhhcCCCeEEEecChhHHHHHHHhhccCCcccceEEEcCCCcceEEEEEccccCCCCcccccee
Q 033009 1 MGR-RILNDALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYIKDFQLYDPHRVGKIKVELLGRVNDCRGLTYRQD 79 (129)
Q Consensus 1 M~~-d~iad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eG~I~~~~~~~~~~~~~i~I~Lky~~~k~~~IspRvy 79 (129)
|+. ||||||||+||||++++|++|.++|+||++.+||++|++||||++|+..+++....++|+|||..+++++||||+|
T Consensus 1 m~~~~~iad~lt~IrNa~~a~~~~v~~~p~Skl~~~il~iL~~eGyI~~~~~~~~~~~~~i~v~Lk~~i~~~~~IS~Rvy 80 (130)
T PLN00146 1 MVRRSVLNDALKTMYNAEKRGKRQVLIRPSSKVVIKFLKVMQKHGYIGEFEVVDDHRSGKIVVELNGRLNKCGVISPRFD 80 (130)
T ss_pred CCCcChHHHHHHHhHhHHHcCCCeEEEEcChHHHHHHHHHHHHCCCCcceEEEecCCcceEEEEEcccccCCcEEEcCEe
Confidence 664 9999999999999999999997339999999999999999999999987766677899999999899999999999
Q ss_pred ccccchhhhhcccCCCCcceEEEEECCCCcccHHHHHhcCCCeEEEEEEC
Q 033009 80 VKAREIEGYTVHALPTRQWGYVVITTPDGVLDHEEALRRNVGGQVLGYFH 129 (129)
Q Consensus 80 ~~~~~l~~~~~~~~p~~~~Gi~IlSTskGimt~~eA~~~~vGGevL~~v~ 129 (129)
++.++||+|..||+|+.|+|++|||||+|||||+||+++++|||+||+||
T Consensus 81 ~~~~~l~~v~~~~~~~~g~Gi~IlSTskGimt~~eAr~~~vGGEvL~~vy 130 (130)
T PLN00146 81 VKVKEIEAWTARLLPSRQFGYIVLTTSAGIMDHEEARRKNVGGKVLGFFY 130 (130)
T ss_pred cCcchhhHHHhccCCCCCCEEEEEECCCccccHHHHHHcCCCCEEEEEEC
Confidence 99999999999999999999999999999999999999999999999998
No 3
>COG0096 RpsH Ribosomal protein S8 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.1e-50 Score=289.71 Aligned_cols=122 Identities=38% Similarity=0.585 Sum_probs=117.5
Q ss_pred CCC-cHHHHHHHHhhhhhhcCCCeEEEecChhHHHHHHHhhccCCcccceEEEcCCCcceEEEEEccccCCCCccc----
Q 033009 1 MGR-RILNDALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYIKDFQLYDPHRVGKIKVELLGRVNDCRGLT---- 75 (129)
Q Consensus 1 M~~-d~iad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eG~I~~~~~~~~~~~~~i~I~Lky~~~k~~~Is---- 75 (129)
|++ ||||||||+||||++++|..|.+ |+||+..+||++|++||||++|++.+++.++.++|+|||+.|++|+|+
T Consensus 1 m~~~DpiAdmltrIrNa~~~~~~~v~~-P~SKl~~~il~vLk~eGYI~~f~~~~~~~~~~~~v~Lky~~n~~~vI~~~~r 79 (132)
T COG0096 1 MMMTDPLADMLTRIRNAERAKKEVVSM-PASKLKGAILKVLKKEGYIKDFEVIDDGRKGKLRVQLKYRINGCGVISPIKR 79 (132)
T ss_pred CccccHHHHHHHHhHhHHHhccceeec-chHHHHHHHHHHHHHcCCcceEEEEeCCcceEEEEEEEeccCCCccccccee
Confidence 665 99999999999999999999997 999999999999999999999999999999999999999999999998
Q ss_pred ---c--ceeccccchhhhhcccCCCCcceEEEEECCCCcccHHHHHhcCCCeEEEEEEC
Q 033009 76 ---Y--RQDVKAREIEGYTVHALPTRQWGYVVITTPDGVLDHEEALRRNVGGQVLGYFH 129 (129)
Q Consensus 76 ---p--Rvy~~~~~l~~~~~~~~p~~~~Gi~IlSTskGimt~~eA~~~~vGGevL~~v~ 129 (129)
| |+|.+.++||++.+ |+|++|||||+|||||+|||++++|||||||||
T Consensus 80 VSkpg~rvy~~~~~LP~v~~------g~Gi~IvSTs~GVMtd~eAr~~~vGGevLcyV~ 132 (132)
T COG0096 80 VSKPGLRVYEKKRELPAVLN------GLGIAIVSTSKGVMTDKEARKKGVGGEVLCYVW 132 (132)
T ss_pred cCCCCceeecChhhhhhhhc------CceEEEEEcCCCccChHHHHHcCCCcEEEEEEC
Confidence 4 89999999999998 799999999999999999999999999999999
No 4
>PRK04034 rps8p 30S ribosomal protein S8P; Reviewed
Probab=100.00 E-value=1.4e-48 Score=280.96 Aligned_cols=128 Identities=40% Similarity=0.660 Sum_probs=121.6
Q ss_pred CC-CcHHHHHHHHhhhhhhcCCCeEE-EecChhHHHHHHHhhccCCcccceEEEcCCCcceEEEEEccccCCCCccccce
Q 033009 1 MG-RRILNDALRAIVNAERRGKATVE-LQPISTVMSSFLNIMKYRGYIKDFQLYDPHRVGKIKVELLGRVNDCRGLTYRQ 78 (129)
Q Consensus 1 M~-~d~iad~lt~IrNa~~a~~~~v~-i~p~Sk~~~~il~iL~~eG~I~~~~~~~~~~~~~i~I~Lky~~~k~~~IspRv 78 (129)
|+ +|+||||||+||||++|+++.|. + |+|+++++||++|++||||++|++.++++++.+.|+|||..+++++|+||+
T Consensus 1 m~~~d~iad~lt~IrNa~~a~~~~v~~~-p~Sk~~~~il~iL~~eGyI~~~~~~~~~~~~~~~v~Lk~~~~~~~~IkPRv 79 (130)
T PRK04034 1 MVLLDPLANALSTIKNAEMVGKKEVIIK-PASKLIGNVLRVMQDEGYIGEFEYIDDGRAGKFKVELLGRINKCGAIKPRY 79 (130)
T ss_pred CCcccHHHHHHHHhHhHHHcCCceEEEE-cccHHHHHHHHHHHHCCCceEEEEEcCCCccceEEEECCccCCCCcCCCCe
Confidence 65 49999999999999999999985 6 999999999999999999999998776667788999999888899999999
Q ss_pred eccccchhhhhcccCCCCcceEEEEECCCCcccHHHHHhcCCCeEEEEEEC
Q 033009 79 DVKAREIEGYTVHALPTRQWGYVVITTPDGVLDHEEALRRNVGGQVLGYFH 129 (129)
Q Consensus 79 y~~~~~l~~~~~~~~p~~~~Gi~IlSTskGimt~~eA~~~~vGGevL~~v~ 129 (129)
|+++++|+++..+++|++|+|++|||||+|||||+||+++++|||+||+||
T Consensus 80 y~~~~~l~~~~~~~l~~~~lGi~IlSTskGImt~~eA~~~~vGGEvL~~v~ 130 (130)
T PRK04034 80 PVKYDEFEKWEKRYLPARDFGILIVSTSKGVMSHKEAREKGIGGVLLAYVY 130 (130)
T ss_pred EcCHhHhHHHHhccCCCCCceEEEEECCCCceeHHHHHHcCCCCEEEEEEC
Confidence 999999999999999999999999999999999999999999999999999
No 5
>CHL00042 rps8 ribosomal protein S8
Probab=100.00 E-value=4.3e-47 Score=273.94 Aligned_cols=122 Identities=25% Similarity=0.364 Sum_probs=113.7
Q ss_pred CCCcHHHHHHHHhhhhhhcCCCeEEEecChhHHHHHHHhhccCCcccceEEEcCCCcceEEEEEccccC-CCCccc----
Q 033009 1 MGRRILNDALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYIKDFQLYDPHRVGKIKVELLGRVN-DCRGLT---- 75 (129)
Q Consensus 1 M~~d~iad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eG~I~~~~~~~~~~~~~i~I~Lky~~~-k~~~Is---- 75 (129)
|.+||||||||+||||++|++.+|.+ |+|+++.+||++|++||||++|++.+++.++.++|+|||+.+ +.|+|+
T Consensus 1 m~~d~iad~lt~IrNa~~a~~~~v~i-p~Skl~~~il~iL~~eGyI~~~~~~~~~~~~~i~v~Lky~~~~~~pvi~~i~~ 79 (132)
T CHL00042 1 MGNDTIADMLTRIRNANMVKKGTVRI-PATNITENIVKILLREGFIENVREHRENNKYFLVLTLKYRGNKKKPYITTLKR 79 (132)
T ss_pred CCcchHHHHHHHhHHHHHCCCCEEEE-eccHHHHHHHHHHHHCCcccceEEEecCCeeEEEEEEEeecCCCceeccccEE
Confidence 77799999999999999999999998 999999999999999999999998877777889999999853 346664
Q ss_pred ---c--ceeccccchhhhhcccCCCCcceEEEEECCCCcccHHHHHhcCCCeEEEEEEC
Q 033009 76 ---Y--RQDVKAREIEGYTVHALPTRQWGYVVITTPDGVLDHEEALRRNVGGQVLGYFH 129 (129)
Q Consensus 76 ---p--Rvy~~~~~l~~~~~~~~p~~~~Gi~IlSTskGimt~~eA~~~~vGGevL~~v~ 129 (129)
| |+|++.++||++.+ |+|++|||||+|||||+||+++++|||+||+||
T Consensus 80 iSkPg~Rvy~~~~~L~~~~~------g~G~~IlSTskGimt~~eA~~~~iGGe~L~~v~ 132 (132)
T CHL00042 80 ISKPGLRIYSNYKEIPRVLG------GMGIVILSTSKGIMTDREARLKGIGGEILCYIW 132 (132)
T ss_pred EcCCCceeEcCHhHHHHHhC------CCcEEEEECCCCcccHHHHHHcCCCCEEEEEEC
Confidence 7 99999999999997 799999999999999999999999999999999
No 6
>PRK00136 rpsH 30S ribosomal protein S8; Validated
Probab=100.00 E-value=1.7e-45 Score=264.95 Aligned_cols=121 Identities=27% Similarity=0.381 Sum_probs=113.0
Q ss_pred CCCcHHHHHHHHhhhhhhcCCCeEEEecChhHHHHHHHhhccCCcccceEEEcCCCcceEEEEEccccCCCCccc-----
Q 033009 1 MGRRILNDALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYIKDFQLYDPHRVGKIKVELLGRVNDCRGLT----- 75 (129)
Q Consensus 1 M~~d~iad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eG~I~~~~~~~~~~~~~i~I~Lky~~~k~~~Is----- 75 (129)
|.+|+||||||+||||+++++.+|.+ |+|+++.+||++|++||||++|++.++++..+++|+|||+.+ +|+|+
T Consensus 1 m~~d~i~d~lt~IrNa~~~~~~~v~i-p~sk~~~~il~iL~~eGyI~~~~~~~~~~~~~~~v~Lky~~~-~pvi~~i~~I 78 (130)
T PRK00136 1 SMTDPIADMLTRIRNAQMAKHETVSM-PASKLKVAIAEILKEEGYIKDYEVEEDGKQGILRITLKYGEG-EPVIEGIKRV 78 (130)
T ss_pred CCcChHHHHHHHHHHHHHcCCCeEEe-cccHHHHHHHHHHHHCCcccceEEEecCCcceEEEEEecCCC-CcccccceEe
Confidence 77799999999999999999999997 999999999999999999999998766556679999999854 68774
Q ss_pred --c--ceeccccchhhhhcccCCCCcceEEEEECCCCcccHHHHHhcCCCeEEEEEEC
Q 033009 76 --Y--RQDVKAREIEGYTVHALPTRQWGYVVITTPDGVLDHEEALRRNVGGQVLGYFH 129 (129)
Q Consensus 76 --p--Rvy~~~~~l~~~~~~~~p~~~~Gi~IlSTskGimt~~eA~~~~vGGevL~~v~ 129 (129)
| |+|++.++|+++.+ |+|++|+|||+|||||+||+++++|||+||+||
T Consensus 79 SkPg~Riy~~~~~l~~~~~------g~G~~IlSTs~Gimt~~eA~~~~iGGeiL~~v~ 130 (130)
T PRK00136 79 SKPGLRVYKKKDELPKVLN------GLGIAIVSTSKGVMTDREARKAGVGGEVLCYVW 130 (130)
T ss_pred cCCCcceEcCHhHHHHHHC------CCCEEEEEcCCCeeeHHHHHHhCCCCEEEEEEC
Confidence 6 99999999999997 799999999999999999999999999999999
No 7
>PF00410 Ribosomal_S8: Ribosomal protein S8; InterPro: IPR000630 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 S8 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S8 is known to bind directly to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [], groups eubacterial, algal and plant chloroplast, cyanelle, archaebacterial and Marchantia polymorpha mitochondrial S8; mammalian and plant S15A; and yeast S22 (S24) ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1S1H_H 3O30_O 3O2Z_O 3IZB_H 3U5G_W 3U5C_W 3OTO_H 1AN7_A 2HGR_K 3BBN_H ....
Probab=100.00 E-value=2.9e-44 Score=257.87 Aligned_cols=119 Identities=34% Similarity=0.479 Sum_probs=110.9
Q ss_pred cHHHHHHHHhhhhhhcCCCeEEEecChhHHHHHHHhhccCCcccceEEEcCCCc-ceEEEEEccccCCCCccc-------
Q 033009 4 RILNDALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYIKDFQLYDPHRV-GKIKVELLGRVNDCRGLT------- 75 (129)
Q Consensus 4 d~iad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eG~I~~~~~~~~~~~-~~i~I~Lky~~~k~~~Is------- 75 (129)
|||||+|++||||+++++++|.+ |+|++++++|++|++||||++|++.+++.+ ++++|+|||+.++.|+|+
T Consensus 1 D~lad~l~~I~Na~~~~~~~v~i-p~sk~~~~il~iL~~eGyI~~f~~~~~~~~~~~i~I~Lky~~~~~~~i~~i~~iSk 79 (129)
T PF00410_consen 1 DPLADLLTRIRNASRARKRFVII-PYSKLNLSILKILKKEGYISGFEIIDDNRNGKRIWIELKYRRNGKPVIKKIKRISK 79 (129)
T ss_dssp SHHHHHHHHHHHHHHTTCSEEEE-EHCHHHHHHHHHHHHTTSEEEEEEEESSSSEEEEEEEESBCSSSSBSSSEEEESSB
T ss_pred CcHHHHHHHhHHHHHCCCCEEEe-cccHHHHHHHHHHhhccccceeEeeccCCCceEEEEEEccccccchhhhhhhcccC
Confidence 89999999999999999999998 999999999999999999999999887764 679999999656667665
Q ss_pred --cceeccccchhhhhcccCCCCcceEEEEECCCCcccHHHHHhcCCCeEEEEEEC
Q 033009 76 --YRQDVKAREIEGYTVHALPTRQWGYVVITTPDGVLDHEEALRRNVGGQVLGYFH 129 (129)
Q Consensus 76 --pRvy~~~~~l~~~~~~~~p~~~~Gi~IlSTskGimt~~eA~~~~vGGevL~~v~ 129 (129)
+|+|++.++|+++.+ |+|++|+|||+||||++||+++++|||+||+||
T Consensus 80 p~~r~y~~~~~L~~~~~------g~g~~IlSTskGImt~~eA~~~~vGGevL~~V~ 129 (129)
T PF00410_consen 80 PGRRVYISYKELPKVKN------GLGILILSTSKGIMTHREARKLNVGGEVLCYVW 129 (129)
T ss_dssp TTCCCEESGTGSHHSCT------TTSEEEEEETTEEEEHHHHHHHTSEEEEEEEEE
T ss_pred CCcceecCHHHHHHHhC------CCeEEEEEcCCCcEeHHHHHHcCCCCEEEEEEC
Confidence 499999999999886 799999999999999999999999999999998
No 8
>KOG1754 consensus 40S ribosomal protein S15/S22 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.5e-40 Score=233.76 Aligned_cols=129 Identities=50% Similarity=0.882 Sum_probs=126.4
Q ss_pred CCC-cHHHHHHHHhhhhhhcCCCeEEEecChhHHHHHHHhhccCCcccceEEEcCCCcceEEEEEccccCCCCcccccee
Q 033009 1 MGR-RILNDALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYIKDFQLYDPHRVGKIKVELLGRVNDCRGLTYRQD 79 (129)
Q Consensus 1 M~~-d~iad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eG~I~~~~~~~~~~~~~i~I~Lky~~~k~~~IspRvy 79 (129)
|+. +.|||+|..|+||.+++|++|.+.|+|+....||.+|.+||||.+|++.+|++++++.|.|..|.|+|++||||+.
T Consensus 1 m~~~~vLaDalksinNA~krGK~qvlirp~Skvii~FL~vmmkhGyIg~fei~ddhragkivv~L~gRlNkcg~Isprfd 80 (130)
T KOG1754|consen 1 MVRMNVLADALKSINNAEKRGKRQVLIRPSSKVIIRFLTVMMKHGYIGEFEIIDDHRAGKIVVNLTGRLNKCGVISPRFD 80 (130)
T ss_pred CchHHHHHHHHHHhhhHHhcCCceEEecccHHHHHHHHHHHHHcCcccceEEecCCccceEEEecccccccccccccccc
Confidence 554 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccchhhhhcccCCCCcceEEEEECCCCcccHHHHHhcCCCeEEEEEEC
Q 033009 80 VKAREIEGYTVHALPTRQWGYVVITTPDGVLDHEEALRRNVGGQVLGYFH 129 (129)
Q Consensus 80 ~~~~~l~~~~~~~~p~~~~Gi~IlSTskGimt~~eA~~~~vGGevL~~v~ 129 (129)
++.++|++|.+..+|++++|+.+++||.|+|+|+||+.+++|||+||++|
T Consensus 81 V~lkdlek~~n~llpsrqfg~ivltts~Gimdh~ear~k~~gg~ilg~~~ 130 (130)
T KOG1754|consen 81 VKLKDLEKWTNSLLPSRQFGYIVLTTSAGIMDHEEARRKNVGGKILGFFY 130 (130)
T ss_pred cccchHHHHHhccCccceeeEEEEecccccccHHHHhHhhcCcccceeeC
Confidence 99999999999999999999999999999999999999999999999998
No 9
>PF09639 YjcQ: YjcQ protein; InterPro: IPR018597 YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is found in bacteria and also in the Lactococcus phage Tuc2009. In bacteria it appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown []. However, it is thought to be the major head protein in viruses [] and is found in prophage in bacteria. ; PDB: 2HGC_A.
Probab=55.06 E-value=5.6 Score=26.38 Aligned_cols=24 Identities=25% Similarity=0.433 Sum_probs=17.9
Q ss_pred hHHHHHHHhhccCCcccceEEEcC
Q 033009 31 TVMSSFLNIMKYRGYIKDFQLYDP 54 (129)
Q Consensus 31 k~~~~il~iL~~eG~I~~~~~~~~ 54 (129)
..-..++.-|.++|||.|+.+...
T Consensus 25 ~~~~~il~~L~d~GyI~G~~~~~~ 48 (88)
T PF09639_consen 25 SYWSDILRMLQDEGYIKGVSVVRY 48 (88)
T ss_dssp HHHHHHHHHHHHHTSEE--EESSS
T ss_pred HHHHHHHHHHHHCCCccceEEEec
Confidence 556678889999999999988654
No 10
>COG2519 GCD14 tRNA(1-methyladenosine) methyltransferase and related methyltransferases [Translation, ribosomal structure and biogenesis]
Probab=49.87 E-value=29 Score=27.84 Aligned_cols=43 Identities=16% Similarity=0.296 Sum_probs=38.1
Q ss_pred HHHHHHHHhhhhhhcCCCeEEEecChhHHHHHHHhhccCCccc
Q 033009 5 ILNDALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYIK 47 (129)
Q Consensus 5 ~iad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eG~I~ 47 (129)
-..|++.++.++.+.+-..|...|+.....+..+.|.+.||+.
T Consensus 173 ~PW~~le~~~~~Lkpgg~~~~y~P~veQv~kt~~~l~~~g~~~ 215 (256)
T COG2519 173 DPWNVLEHVSDALKPGGVVVVYSPTVEQVEKTVEALRERGFVD 215 (256)
T ss_pred ChHHHHHHHHHHhCCCcEEEEEcCCHHHHHHHHHHHHhcCccc
Confidence 3568899999999999888877899999999999999998865
No 11
>PF08438 MMR_HSR1_C: GTPase of unknown function C-terminal; InterPro: IPR013646 This domain is found at the C terminus of IPR002917 from INTERPRO in archaeal and eukaryotic GTP-binding proteins. ; PDB: 1WXQ_A.
Probab=48.03 E-value=30 Score=24.19 Aligned_cols=37 Identities=14% Similarity=0.163 Sum_probs=23.5
Q ss_pred HHHHHHhhhhhhcCCCeEEEecChhHHHHHHHhhccCCccc
Q 033009 7 NDALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYIK 47 (129)
Q Consensus 7 ad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eG~I~ 47 (129)
.+.+.+|+..+ .....+ |.|-..+-.|+-+.++|||+
T Consensus 11 ~~ni~kl~~~~---~~~~vV-p~SA~aEl~Lr~a~k~g~I~ 47 (109)
T PF08438_consen 11 DENIEKLKEKY---PDEPVV-PTSAAAELALRKAAKAGLID 47 (109)
T ss_dssp HHHHHHHHHHH---TT-EEE-EE-HHHHHHHHS-SSS----
T ss_pred HhHHHHHHHhC---CCCcee-eccHHHHHHHHHHHHCCCEE
Confidence 46677888755 333444 99999999999999999998
No 12
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=47.64 E-value=9 Score=25.44 Aligned_cols=36 Identities=14% Similarity=0.179 Sum_probs=31.7
Q ss_pred HHHhhhhhhcCCCeEEEecChhHHHHHHHhhccCCcc
Q 033009 10 LRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYI 46 (129)
Q Consensus 10 lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eG~I 46 (129)
..+|+++.+..-..+.+ |+......-|.-|.+||.|
T Consensus 32 ~E~l~~~L~~~yp~i~~-Ps~e~l~~~L~~Li~erkI 67 (80)
T PF10264_consen 32 QETLREHLRKHYPGIAI-PSQEVLYNTLGTLIKERKI 67 (80)
T ss_pred HHHHHHHHHHhCCCCCC-CCHHHHHHHHHHHHHcCce
Confidence 45778888888888887 9999999999999999987
No 13
>PF09879 DUF2106: Predicted membrane protein (DUF2106); InterPro: IPR011313 [NiFe] hydrogenases function in H2 metabolism in a variety of microorganisms, enabling them to use H2 as a source of reducing equivalent under aerobic and anaerobic conditions [NiFe] hydrogenases consist of two subunits, hydrogenase large and hydrogenase small. The large subunit contains the binuclear [NiFe] active site, while the small subunit binds at least one [4Fe-4S] cluster []. Energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type) form a distinct group within the [NiFe] hydrogenase family [, ]. Members of this subgroup include: Hydrogenase 3 and 4 (Hyc and Hyf) from Escherichia coli CO-induced hydrogenase (Coo) from Rhodospirillum rubrum Mbh hydrogenase from Pyrococcus furiosus Eha and Ehb hydrogenases from Methanothermobacter species Ech hydrogenase from Methanosarcina barkeri Energy-converting [NiFe] hydrogenases are membrane-bound enzymes with a six-subunit core: the large and small hydrogenase subunits, plus two hydrophilic proteins and two integral membrane proteins. Their large and small subunits show little sequence similarity to other [NiFe] hydrogenases, except for key conserved residues coordinating the active site and [FeS] cluster. However, they show considerable sequence similarity to the six-subunit, energy-conserving NADH:quinone oxidoreductases (complex I), which are present in cytoplasmic membranes of many bacteria and in inner mitochondrial membranes. However, the reactions they catalyse differ significantly from complex I. Energy-converting [NiFe] hydrogenases function as ion pumps. Eha and Ehb hydrogenases contain extra subunits in addition to those shared by other energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type). Eha contains a 6[4Fe-4S] polyferredoxin, a 10[4F-4S] polyferredoxin, ten other predicted integral membrane proteins (EhaA IPR011306 from INTERPRO, EhaB IPR011314 from INTERPRO, EhaC IPR011316 from INTERPRO, EhaD IPR011308 from INTERPRO, EhaE IPR011317 from INTERPRO, EhaF IPR011313 from INTERPRO, EhaG IPR011311 from INTERPRO, EhaI IPR011318 from INTERPRO, EhaK IPR011319 from INTERPRO, EhaL IPR011305 from INTERPRO) and four hydrophobic subunits (EhaM, EhaR IPR014502 from INTERPRO, EhS, EhT) []. The ten predicted integral membrane proteins are absent from Ech, Coo, Hyc and Hyf complexes, which may have simpler membrane components than Eha. Eha and Ehb catalyse the reduction of low-potential redox carriers (e.g. ferredoxins or polyferredoxins), which then might function as electron donors to oxidoreductases. Based on sequence similarity and genome context analysis, other organisms such as Methanopyrus kandleri, Methanocaldococcus jannaschii, and Methanothermobacter marburgensis also encode Eha-like [NiFe]-hydrogenase-3-type complexes and have very similar eha operon structure. This entry represents small membrane proteins that are predicted to be the EhaF transmembrane subunits of multi-subunit membrane-bound [NiFe]-hydrogenase Eha complexes.
Probab=43.17 E-value=11 Score=27.76 Aligned_cols=17 Identities=29% Similarity=0.776 Sum_probs=14.5
Q ss_pred CcceEEEEECCCCcccH
Q 033009 96 RQWGYVVITTPDGVLDH 112 (129)
Q Consensus 96 ~~~Gi~IlSTskGimt~ 112 (129)
.=+|..|+||+.||++.
T Consensus 105 ~y~GTTIvS~PGGIlDE 121 (153)
T PF09879_consen 105 PYFGTTIVSHPGGILDE 121 (153)
T ss_pred ccccceEecCCChhHHH
Confidence 34899999999999874
No 14
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=38.66 E-value=44 Score=20.99 Aligned_cols=32 Identities=19% Similarity=0.360 Sum_probs=25.5
Q ss_pred CeEEEecChhHHHHHHHhhccCCcccceEEEcC
Q 033009 22 ATVELQPISTVMSSFLNIMKYRGYIKDFQLYDP 54 (129)
Q Consensus 22 ~~v~i~p~Sk~~~~il~iL~~eG~I~~~~~~~~ 54 (129)
-.+.+ .......++|+.|.++|+|.+|+...+
T Consensus 43 ~~i~l-~~~~~~~~ll~~l~~~g~I~~f~~~~P 74 (84)
T PF13732_consen 43 LRIKL-EDEETANELLQELIEKGIIRSFEEEEP 74 (84)
T ss_pred EEEEE-CCcccHHHHHHHHHhCCCeeEEEEcCC
Confidence 35555 667778999999999999999987643
No 15
>PHA02943 hypothetical protein; Provisional
Probab=36.49 E-value=44 Score=25.03 Aligned_cols=24 Identities=8% Similarity=0.123 Sum_probs=19.8
Q ss_pred ChhHHHHHHHhhccCCcccceEEE
Q 033009 29 ISTVMSSFLNIMKYRGYIKDFQLY 52 (129)
Q Consensus 29 ~Sk~~~~il~iL~~eG~I~~~~~~ 52 (129)
+-.....+|.+|.+||+|+.++++
T Consensus 37 S~~qa~~~LyvLErEG~VkrV~~G 60 (165)
T PHA02943 37 SHSMARNALYQLAKEGMVLKVEIG 60 (165)
T ss_pred CHHHHHHHHHHHHHcCceEEEeec
Confidence 345677899999999999998764
No 16
>COG1244 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=36.46 E-value=44 Score=27.99 Aligned_cols=41 Identities=22% Similarity=0.468 Sum_probs=36.2
Q ss_pred cHHHHHHHHhhhhhhcCCCeEEEecChhHHHHHHHhhccCCc
Q 033009 4 RILNDALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGY 45 (129)
Q Consensus 4 d~iad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eG~ 45 (129)
+.|.|++..|+ |...+-..|++-|.+-..-.+.+-|++.|.
T Consensus 221 eAI~D~i~Si~-~~~~~~d~iSinptnVqKgTlvE~lw~~g~ 261 (358)
T COG1244 221 EAIEDVISSIV-AAKPGTDTISINPTNVQKGTLVEKLWRRGL 261 (358)
T ss_pred HHHHHHHHHHH-HhccCCCeEEecccccchhhHHHHHHHcCC
Confidence 57899999999 888999999998998888889999988875
No 17
>PHA02745 hypothetical protein; Provisional
Probab=33.51 E-value=28 Score=27.84 Aligned_cols=47 Identities=15% Similarity=0.072 Sum_probs=29.8
Q ss_pred CCcccceEEEcCCCcceEEEEEccccCCCCccc--c--ceeccccchhhhh
Q 033009 43 RGYIKDFQLYDPHRVGKIKVELLGRVNDCRGLT--Y--RQDVKAREIEGYT 89 (129)
Q Consensus 43 eG~I~~~~~~~~~~~~~i~I~Lky~~~k~~~Is--p--Rvy~~~~~l~~~~ 89 (129)
++-+..|..=++=...--.=.||||.++++++. | .||++..+|....
T Consensus 120 ~~~~~~f~LPPeYDpnDsRWTLKyR~~~pGLVEL~P~SgVYV~~~~L~~C~ 170 (265)
T PHA02745 120 RQQIRKFTLPPEYDPNDSRWTLKHRYPGSGLVELLPHSGVYINAINLSNCK 170 (265)
T ss_pred hccceeEecCCCCCCCCCcceeeccCCCCCcEEeecCCceEEeHHHHHHHH
Confidence 455555654221011122346999999988888 6 8999998886533
No 18
>PF02813 Retro_M: Retroviral M domain; InterPro: IPR004028 The Gag polyprotein directs the assembly and release of virus particles from infected cells. The Gag polyprotein has three domains required for activity: an N-terminal membrane-binding (M) domain that directs Gag to the plasma membrane, an interaction (I) domain involved in Gag aggregation, and a late assembly (L) domain that mediates the budding process []. During viral maturation, the Gag polyprotein is then cleaved into major structural proteins by the viral protease, yielding the matrix, capsid, nucleoprotein, and some smaller peptides. In Rous sarcoma virus (RSV), the M domain consists of the first 85 residues of the matrix protein. However, unlike other Gag polyproteins, the M domain of RSV Gag is not myristylated, but retains full activity [].This domain forms an alpha helical bundle structure []. This entry represents the M domain of the Gag polyprotein found in avian retroviruses. This entry also identifies Gag polyproteins from several avian endogenous retroviruses, which arise when one or more copies of the retroviral genome becomes integrated into the host genome [].; PDB: 1A6S_A.
Probab=29.24 E-value=41 Score=22.42 Aligned_cols=22 Identities=14% Similarity=0.398 Sum_probs=17.7
Q ss_pred cChhHHHHHHHhhccCCcccce
Q 033009 28 PISTVMSSFLNIMKYRGYIKDF 49 (129)
Q Consensus 28 p~Sk~~~~il~iL~~eG~I~~~ 49 (129)
|++|-+-++|..|.+||.+.+=
T Consensus 20 ps~Kei~a~Ls~L~~Eg~L~sP 41 (86)
T PF02813_consen 20 PSKKEIGAMLSLLQKEGLLTSP 41 (86)
T ss_dssp S-SSHHHHHHHTGGGTT-TT-G
T ss_pred CcHHHHHHHHHHHHHccCcCCh
Confidence 8999999999999999999864
No 19
>COG1591 Holliday junction resolvase - archaeal type [DNA replication, recombination, and repair]
Probab=27.10 E-value=1.2e+02 Score=22.05 Aligned_cols=56 Identities=13% Similarity=0.128 Sum_probs=36.8
Q ss_pred ChhHHHHHHHhhccCCccc------c------eEEEcCCCcceEEEEEccccCCCCccccceeccccchhhhhc
Q 033009 29 ISTVMSSFLNIMKYRGYIK------D------FQLYDPHRVGKIKVELLGRVNDCRGLTYRQDVKAREIEGYTV 90 (129)
Q Consensus 29 ~Sk~~~~il~iL~~eG~I~------~------~~~~~~~~~~~i~I~Lky~~~k~~~IspRvy~~~~~l~~~~~ 90 (129)
-|..=.++.++|+++||=- + ..+.--+..-.+.|+.|++-.. ++|++.+++.++..
T Consensus 6 G~~~EReLv~~L~e~GfAvvR~paSG~sk~p~pDivA~~g~~~l~iE~K~~~~~------kiYl~~e~ve~L~~ 73 (137)
T COG1591 6 GSRFERELVRILWERGFAVVRAPASGGSKRPLPDIVAGNGGVYLAIEVKSRRET------KIYLDKEQVEKLVE 73 (137)
T ss_pred cchHHHHHHHHHHhcCceEEEcccCCCCCCCCCCEEecCCCEEEEEEEEeccCC------cEEEcHHHHHHHHH
Confidence 3556678999999999842 2 0011112335789999987422 77999999887654
No 20
>COG4037 Predicted membrane protein [Function unknown]
Probab=26.07 E-value=32 Score=25.22 Aligned_cols=18 Identities=33% Similarity=0.787 Sum_probs=15.0
Q ss_pred CcceEEEEECCCCcccHH
Q 033009 96 RQWGYVVITTPDGVLDHE 113 (129)
Q Consensus 96 ~~~Gi~IlSTskGimt~~ 113 (129)
.-+|..|+|++.||++.-
T Consensus 109 ~yfGTtIvS~PGGilDEI 126 (163)
T COG4037 109 RYFGTTIVSHPGGILDEI 126 (163)
T ss_pred EEcccEEecCCChhHHHH
Confidence 458999999999998753
No 21
>PF09572 RE_XamI: XamI restriction endonuclease; InterPro: IPR019072 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the XamI restriction endonuclease which recognises GTCGAC but cleavage site unknown. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=23.70 E-value=73 Score=25.54 Aligned_cols=32 Identities=34% Similarity=0.459 Sum_probs=25.5
Q ss_pred HHHH-HHHH-----hhhhhhcCCCeEEEecChhHHHHHHHhhccCCccc
Q 033009 5 ILND-ALRA-----IVNAERRGKATVELQPISTVMSSFLNIMKYRGYIK 47 (129)
Q Consensus 5 ~iad-~lt~-----IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eG~I~ 47 (129)
.++| +|.. +|||+.+| +-..|.+.|...||-+
T Consensus 103 ivadrL~~avA~piiRnaqErR-----------Qe~~i~~~L~~~GYt~ 140 (251)
T PF09572_consen 103 IVADRLCGAVADPIIRNAQERR-----------QEAAIAEWLEARGYTK 140 (251)
T ss_pred HHHHHHHhhhcchHHHhHHHHH-----------HHHHHHHHHHhcCceE
Confidence 4566 7888 99999997 4557788899999875
No 22
>PF02618 YceG: YceG-like family; InterPro: IPR003770 This uncharacterised protein family, found in three of four microbial genomes, virtually always once per genome, includes YceG from Escherichia coli. Proteins in this family are typically between 332 and 389 amino acids in length. This protein is encoded next to PabC, 4-amino-4-deoxychorismate lyase, in Escherichia coli and numerous other proteobacteria, but that proximity is not conserved in other lineages. Numerous members of this family have been misannotated as aminodeoxychorismate lyase, apparently because of promiximty to PabC. The structure of Swiss:P28306 was solved by X-ray crystallography. This group represents an uncharacterised protein family UPF0755.; PDB: 2R1F_B.
Probab=22.28 E-value=1.3e+02 Score=24.24 Aligned_cols=44 Identities=11% Similarity=0.160 Sum_probs=28.5
Q ss_pred HHHHHHHHhhhhhhcCCCeEEEecChhHHHHHHHhhccCCcccceE
Q 033009 5 ILNDALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYIKDFQ 50 (129)
Q Consensus 5 ~iad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eG~I~~~~ 50 (129)
+..+++..|.++..... .|.| |.-.-..+|++.|.+.|.+..-.
T Consensus 55 S~~eil~~L~~g~~~~~-~vTI-pEG~t~~~i~~~l~~~~~~~~~~ 98 (297)
T PF02618_consen 55 SYKEILSILTSGKVAQV-RVTI-PEGFTLEQIAQRLAEKGGISKED 98 (297)
T ss_dssp -HHHHHHHHHH-----E-EEEE--TT--HHHHHHHHHCSTTEE---
T ss_pred CHHHHHHHHHhccccee-EEEe-cCCCcHHHHHHHHHhccCCCHHH
Confidence 57789999988877764 7887 99999999999999999995443
No 23
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=21.99 E-value=1.2e+02 Score=19.50 Aligned_cols=24 Identities=13% Similarity=0.234 Sum_probs=15.1
Q ss_pred cChhHHHHHHHhhccCCcccceEEE
Q 033009 28 PISTVMSSFLNIMKYRGYIKDFQLY 52 (129)
Q Consensus 28 p~Sk~~~~il~iL~~eG~I~~~~~~ 52 (129)
+.+++. .-|+.|.++|||+--...
T Consensus 27 t~g~Ls-~hL~~Le~~GyV~~~k~~ 50 (80)
T PF13601_consen 27 TDGNLS-KHLKKLEEAGYVEVEKEF 50 (80)
T ss_dssp -HHHHH-HHHHHHHHTTSEEEEEE-
T ss_pred CHHHHH-HHHHHHHHCCCEEEEEec
Confidence 344444 446779999999965443
No 24
>PRK15453 phosphoribulokinase; Provisional
Probab=21.81 E-value=1e+02 Score=25.11 Aligned_cols=33 Identities=15% Similarity=0.038 Sum_probs=28.3
Q ss_pred HHHHHHhhhhhhcCCCeEEEecChhHHHHHHHhh
Q 033009 7 NDALRAIVNAERRGKATVELQPISTVMSSFLNIM 40 (129)
Q Consensus 7 ad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL 40 (129)
.-+|+-|.++.|++...+.+ |-.|+-++.--||
T Consensus 243 ~yl~~~~~~~~~s~~~~~v~-~g~~~~~a~~~i~ 275 (290)
T PRK15453 243 PYLLSMIQGSFMSRANTIVV-PGGKMGLAMELIL 275 (290)
T ss_pred HHHHHHhccchhcCCCcEEe-cCchHHHHHHHHH
Confidence 46899999999999999997 9999988765554
No 25
>cd02029 PRK_like Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.
Probab=21.14 E-value=1.1e+02 Score=24.87 Aligned_cols=34 Identities=12% Similarity=0.060 Sum_probs=29.0
Q ss_pred HHHHHHHhhhhhhcCCCeEEEecChhHHHHHHHhh
Q 033009 6 LNDALRAIVNAERRGKATVELQPISTVMSSFLNIM 40 (129)
Q Consensus 6 iad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL 40 (129)
..-+|+-|.++.|++...+.+ |-.|+-++.--||
T Consensus 236 ~~~~~~~~~~~~~s~~~~~v~-~g~~~~~a~~~i~ 269 (277)
T cd02029 236 FPYLLNMLHDSFMSRPNTIVV-PGGKMGLAMELIL 269 (277)
T ss_pred HHHHHHhhccchhcCCCcEEe-cCchHHHHHHHHH
Confidence 356899999999999999997 9999988876554
No 26
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=20.78 E-value=1.6e+02 Score=19.50 Aligned_cols=41 Identities=12% Similarity=0.061 Sum_probs=26.5
Q ss_pred HHHHHHhhhhhhcCCCeEEEecChhHHHHHHHhhccCCcccceEEE
Q 033009 7 NDALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYIKDFQLY 52 (129)
Q Consensus 7 ad~lt~IrNa~~a~~~~v~i~p~Sk~~~~il~iL~~eG~I~~~~~~ 52 (129)
.++...|++-. ..... +.......+|+-|.++|+|......
T Consensus 21 Yei~~~l~~~~---~~~~~--i~~gtlY~~L~rLe~~GlI~~~~~~ 61 (100)
T TIGR03433 21 YGIAQRIQQIS---EDVLQ--VEEGSLYPALHRLERRGWIAAEWGE 61 (100)
T ss_pred HHHHHHHHHHc---CCccc--cCCCcHHHHHHHHHHCCCeEEEeee
Confidence 34555565532 22334 3445678899999999999986443
No 27
>PF08643 DUF1776: Fungal family of unknown function (DUF1776); InterPro: IPR013952 This is a fungal protein of unknown function. One of the proteins P32792 from SWISSPROT has been localised to the mitochondria [].
Probab=20.05 E-value=84 Score=25.69 Aligned_cols=33 Identities=21% Similarity=0.297 Sum_probs=25.5
Q ss_pred cCCCeEEE--ecChhHHHHHHHhhccCCcccceEE
Q 033009 19 RGKATVEL--QPISTVMSSFLNIMKYRGYIKDFQL 51 (129)
Q Consensus 19 a~~~~v~i--~p~Sk~~~~il~iL~~eG~I~~~~~ 51 (129)
||++-|.+ -|+..+...++.=|++.|||==+..
T Consensus 1 aR~evVvI~Gs~~~PltR~la~DLeRRGFIV~v~~ 35 (299)
T PF08643_consen 1 ARKEVVVIAGSPHDPLTRSLALDLERRGFIVYVTV 35 (299)
T ss_pred CceeEEEEECCCCCccHHHHHHHHhhCCeEEEEEe
Confidence 34555554 4889999999999999999975444
Done!