Query psy13245
Match_columns 130
No_of_seqs 124 out of 1045
Neff 6.6
Searched_HMMs 46136
Date Fri Aug 16 23:50:27 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13245.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13245hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00146 40S ribosomal protein 100.0 1.5E-51 3.3E-56 296.0 14.3 130 1-130 1-130 (130)
2 PTZ00158 40S ribosomal protein 100.0 3.1E-51 6.6E-56 294.0 13.7 129 1-130 1-130 (130)
3 COG0096 RpsH Ribosomal protein 100.0 1.2E-50 2.6E-55 290.4 12.8 123 1-130 1-132 (132)
4 PRK04034 rps8p 30S ribosomal p 100.0 1.1E-49 2.5E-54 286.3 14.6 130 1-130 1-130 (130)
5 CHL00042 rps8 ribosomal protei 100.0 3.7E-46 7.9E-51 268.7 13.2 121 3-130 2-132 (132)
6 PRK00136 rpsH 30S ribosomal pr 100.0 1.7E-44 3.6E-49 259.5 13.4 120 3-130 2-130 (130)
7 PF00410 Ribosomal_S8: Ribosom 100.0 3.5E-43 7.5E-48 252.0 12.7 119 5-130 1-129 (129)
8 KOG1754|consensus 100.0 2.8E-38 6.1E-43 222.8 11.1 130 1-130 1-130 (130)
9 PF09639 YjcQ: YjcQ protein; 67.0 4.6 9.9E-05 26.8 1.9 24 32-55 25-48 (88)
10 COG2519 GCD14 tRNA(1-methylade 50.3 26 0.00057 28.1 3.9 42 7-48 174-215 (256)
11 PHA02745 hypothetical protein; 38.4 28 0.0006 27.8 2.3 46 44-89 120-169 (265)
12 PHA02943 hypothetical protein; 37.7 48 0.001 24.8 3.4 21 33-53 40-60 (165)
13 PF13732 DUF4162: Domain of un 35.9 71 0.0015 20.0 3.7 29 26-54 45-73 (84)
14 PF09879 DUF2106: Predicted me 34.1 19 0.00041 26.6 0.7 16 98-113 106-121 (153)
15 PF13601 HTH_34: Winged helix 33.5 89 0.0019 20.1 3.9 18 36-53 33-50 (80)
16 TIGR03433 padR_acidobact trans 29.3 1.5E+02 0.0033 19.5 4.6 26 29-54 37-62 (100)
17 PF01022 HTH_5: Bacterial regu 27.2 46 0.001 18.9 1.5 14 36-49 34-47 (47)
18 PF14947 HTH_45: Winged helix- 26.3 43 0.00092 21.3 1.4 43 4-49 5-51 (77)
19 PF08643 DUF1776: Fungal famil 26.2 76 0.0016 25.9 3.1 33 21-54 2-37 (299)
20 PF08438 MMR_HSR1_C: GTPase of 25.3 79 0.0017 22.0 2.7 37 8-48 11-47 (109)
21 KOG3877|consensus 25.2 42 0.00092 27.9 1.4 41 4-49 157-198 (393)
22 COG1244 Predicted Fe-S oxidore 23.7 1.3E+02 0.0027 25.4 3.9 41 5-46 221-261 (358)
23 PF10264 Stork_head: Winged he 22.4 82 0.0018 20.8 2.2 36 11-47 32-67 (80)
24 KOG3467|consensus 22.1 1.4E+02 0.003 20.3 3.2 32 5-46 65-96 (103)
25 PRK00111 hypothetical protein; 21.8 81 0.0018 23.9 2.3 24 1-24 1-24 (180)
26 PF09339 HTH_IclR: IclR helix- 21.4 91 0.002 17.9 2.1 17 33-49 34-50 (52)
27 PF02082 Rrf2: Transcriptional 21.2 86 0.0019 19.9 2.1 20 32-51 40-59 (83)
No 1
>PLN00146 40S ribosomal protein S15a; Provisional
Probab=100.00 E-value=1.5e-51 Score=296.00 Aligned_cols=130 Identities=78% Similarity=1.294 Sum_probs=123.9
Q ss_pred CCccchHHHHHHHhHhhhhhCCceEEEEeccchHHHHHHHHhhcCceeeEEEEcCCCCceEEEEeecccCcCccccccee
Q psy13245 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGYIGEFEIVDDHRAGKIVVNLKGRLNKCGVISPRFD 80 (130)
Q Consensus 1 m~~~d~iad~lt~IrNa~~~~~~~~v~~p~sk~~~~il~iL~~eG~I~~~~~~~~~~~~~i~i~Lky~~~~~~~IspRvy 80 (130)
|+++||||||||+||||+++++.+|..+|+||++++|+++|++||||++|++.+++..+.++++|||..+++++||||+|
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 89999999999999999999999953479999999999999999999999987766667899999999999999999999
Q ss_pred ecccchhhhhhCccCCCCceEEEEecCCccccHHHHHHcCCCeEEEEEEC
Q psy13245 81 VPIRHIEKWTNNLLPSRQFGYVVLTTSGGIMDHEEARRKHLGGKILGFFF 130 (130)
Q Consensus 81 ~~~~~i~~~~~~~~p~~~~Gi~IlSTskGimt~~eA~~~~vGGevL~~V~ 130 (130)
++++||++|.+|++|++|+|++|+|||+|||||+||+++++|||+||+||
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 2
>PTZ00158 40S ribosomal protein S15A; Provisional
Probab=100.00 E-value=3.1e-51 Score=294.00 Aligned_cols=129 Identities=79% Similarity=1.255 Sum_probs=123.6
Q ss_pred CCccchHHHHHHHhHhhhhhCCceEEEE-eccchHHHHHHHHhhcCceeeEEEEcCCCCceEEEEeecccCcCcccccce
Q psy13245 1 MVRVNVLSDALKSINNAEKRGKRQVLIR-PCSKVIVKFLTVMMKHGYIGEFEIVDDHRAGKIVVNLKGRLNKCGVISPRF 79 (130)
Q Consensus 1 m~~~d~iad~lt~IrNa~~~~~~~~v~~-p~sk~~~~il~iL~~eG~I~~~~~~~~~~~~~i~i~Lky~~~~~~~IspRv 79 (130)
|+++|+||||||+||||++++|.+| .+ |+||++++||++|++||||++|++.+++..+.+.++|+.+.++|+.||||+
T Consensus 1 m~~~~~iadmlt~IrNa~~~~~~~V-~v~p~Skl~~~il~IL~~eGyI~~~~~~~~~~~~~i~v~l~~rIsk~g~IS~Rv 79 (130)
T PTZ00158 1 MVRMSVLADCLRSIVNAEKQGKRQV-LIRPSSKVVVKFLQVMQKHGYIGEFEIVDDHRSGKIVVNLNGRLNKCGVISPRF 79 (130)
T ss_pred CCcccHHHHHHHhhhhHHhCCCCeE-EEeCCcHHHHHHHHHHHHCCcccceEEEecCCEEEEEEEEcCccccCCCCccce
Confidence 8889999999999999999999995 65 999999999999999999999998777666688999999999999999999
Q ss_pred eecccchhhhhhCccCCCCceEEEEecCCccccHHHHHHcCCCeEEEEEEC
Q psy13245 80 DVPIRHIEKWTNNLLPSRQFGYVVLTTSGGIMDHEEARRKHLGGKILGFFF 130 (130)
Q Consensus 80 y~~~~~i~~~~~~~~p~~~~Gi~IlSTskGimt~~eA~~~~vGGevL~~V~ 130 (130)
|++++|||+|.+|++|.+|+|++|+|||+|||||+||+++++|||+||+||
T Consensus 80 Y~~~~~ip~v~~~~lp~~glGi~IlSTSkGImt~~eAr~~~vGGEvLc~v~ 130 (130)
T PTZ00158 80 DVTLGEFEKWANNILPSRQFGHVVLTTSYGIMDHEEARRRHTGGKILGFFY 130 (130)
T ss_pred ECCcchhhHHhcCCCccccceEEEEECCCCccChHHHHHcCCCceEEEEEC
Confidence 999999999999999999999999999999999999999999999999998
No 3
>COG0096 RpsH Ribosomal protein S8 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-50 Score=290.39 Aligned_cols=123 Identities=41% Similarity=0.684 Sum_probs=115.6
Q ss_pred CCccchHHHHHHHhHhhhhhCCceEEEEeccchHHHHHHHHhhcCceeeEEEEcCCCCceEEEEeecccCcCcccc----
Q psy13245 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGYIGEFEIVDDHRAGKIVVNLKGRLNKCGVIS---- 76 (130)
Q Consensus 1 m~~~d~iad~lt~IrNa~~~~~~~~v~~p~sk~~~~il~iL~~eG~I~~~~~~~~~~~~~i~i~Lky~~~~~~~Is---- 76 (130)
|+|+|||||||||||||+++++.. +.+|+||+..+||++|++||||++|++.++++++.++|+|||+.+++++|+
T Consensus 1 m~~~DpiAdmltrIrNa~~~~~~~-v~~P~SKl~~~il~vLk~eGYI~~f~~~~~~~~~~~~v~Lky~~n~~~vI~~~~r 79 (132)
T COG0096 1 MMMTDPLADMLTRIRNAERAKKEV-VSMPASKLKGAILKVLKKEGYIKDFEVIDDGRKGKLRVQLKYRINGCGVISPIKR 79 (132)
T ss_pred CccccHHHHHHHHhHhHHHhccce-eecchHHHHHHHHHHHHHcCCcceEEEEeCCcceEEEEEEEeccCCCccccccee
Confidence 899999999999999999997776 789999999999999999999999999999999999999999988888876
Q ss_pred ---c--ceeecccchhhhhhCccCCCCceEEEEecCCccccHHHHHHcCCCeEEEEEEC
Q psy13245 77 ---P--RFDVPIRHIEKWTNNLLPSRQFGYVVLTTSGGIMDHEEARRKHLGGKILGFFF 130 (130)
Q Consensus 77 ---p--Rvy~~~~~i~~~~~~~~p~~~~Gi~IlSTskGimt~~eA~~~~vGGevL~~V~ 130 (130)
| |+|.+.++||++.+| +|++|||||+|||||+|||++|+|||||||||
T Consensus 80 VSkpg~rvy~~~~~LP~v~~g------~Gi~IvSTs~GVMtd~eAr~~~vGGevLcyV~ 132 (132)
T COG0096 80 VSKPGLRVYEKKRELPAVLNG------LGIAIVSTSKGVMTDKEARKKGVGGEVLCYVW 132 (132)
T ss_pred cCCCCceeecChhhhhhhhcC------ceEEEEEcCCCccChHHHHHcCCCcEEEEEEC
Confidence 5 888888888888765 99999999999999999999999999999998
No 4
>PRK04034 rps8p 30S ribosomal protein S8P; Reviewed
Probab=100.00 E-value=1.1e-49 Score=286.31 Aligned_cols=130 Identities=50% Similarity=0.913 Sum_probs=123.5
Q ss_pred CCccchHHHHHHHhHhhhhhCCceEEEEeccchHHHHHHHHhhcCceeeEEEEcCCCCceEEEEeecccCcCccccccee
Q psy13245 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGYIGEFEIVDDHRAGKIVVNLKGRLNKCGVISPRFD 80 (130)
Q Consensus 1 m~~~d~iad~lt~IrNa~~~~~~~~v~~p~sk~~~~il~iL~~eG~I~~~~~~~~~~~~~i~i~Lky~~~~~~~IspRvy 80 (130)
|+|+|+||||||+||||++|++.+|+.+|+|+++++||++|++||||++|++.++++++.+.++|||..+++++|+||+|
T Consensus 1 m~~~d~iad~lt~IrNa~~a~~~~v~~~p~Sk~~~~il~iL~~eGyI~~~~~~~~~~~~~~~v~Lk~~~~~~~~IkPRvy 80 (130)
T PRK04034 1 MVLLDPLANALSTIKNAEMVGKKEVIIKPASKLIGNVLRVMQDEGYIGEFEYIDDGRAGKFKVELLGRINKCGAIKPRYP 80 (130)
T ss_pred CCcccHHHHHHHHhHhHHHcCCceEEEEcccHHHHHHHHHHHHCCCceEEEEEcCCCccceEEEECCccCCCCcCCCCeE
Confidence 77789999999999999999999965699999999999999999999999988776677899999998888889999999
Q ss_pred ecccchhhhhhCccCCCCceEEEEecCCccccHHHHHHcCCCeEEEEEEC
Q psy13245 81 VPIRHIEKWTNNLLPSRQFGYVVLTTSGGIMDHEEARRKHLGGKILGFFF 130 (130)
Q Consensus 81 ~~~~~i~~~~~~~~p~~~~Gi~IlSTskGimt~~eA~~~~vGGevL~~V~ 130 (130)
++++||+++..+++|.+|+|++|+|||+|||||+||+++++|||+||+||
T Consensus 81 ~~~~~l~~~~~~~l~~~~lGi~IlSTskGImt~~eA~~~~vGGEvL~~v~ 130 (130)
T PRK04034 81 VKYDEFEKWEKRYLPARDFGILIVSTSKGVMSHKEAREKGIGGVLLAYVY 130 (130)
T ss_pred cCHhHhHHHHhccCCCCCceEEEEECCCCceeHHHHHHcCCCCEEEEEEC
Confidence 99999999999999999999999999999999999999999999999998
No 5
>CHL00042 rps8 ribosomal protein S8
Probab=100.00 E-value=3.7e-46 Score=268.74 Aligned_cols=121 Identities=30% Similarity=0.459 Sum_probs=110.3
Q ss_pred ccchHHHHHHHhHhhhhhCCceEEEEeccchHHHHHHHHhhcCceeeEEEEcCCCCceEEEEeecccC-cCc------cc
Q psy13245 3 RVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGYIGEFEIVDDHRAGKIVVNLKGRLN-KCG------VI 75 (130)
Q Consensus 3 ~~d~iad~lt~IrNa~~~~~~~~v~~p~sk~~~~il~iL~~eG~I~~~~~~~~~~~~~i~i~Lky~~~-~~~------~I 75 (130)
|+|+||||||+||||++|++.+ |.+|+|+++++||++|++||||++|++.+++++++++|+|||+.+ +.| .|
T Consensus 2 ~~d~iad~lt~IrNa~~a~~~~-v~ip~Skl~~~il~iL~~eGyI~~~~~~~~~~~~~i~v~Lky~~~~~~pvi~~i~~i 80 (132)
T CHL00042 2 GNDTIADMLTRIRNANMVKKGT-VRIPATNITENIVKILLREGFIENVREHRENNKYFLVLTLKYRGNKKKPYITTLKRI 80 (132)
T ss_pred CcchHHHHHHHhHHHHHCCCCE-EEEeccHHHHHHHHHHHHCCcccceEEEecCCeeEEEEEEEeecCCCceeccccEEE
Confidence 5699999999999999999999 578999999999999999999999999877777789999999853 234 34
Q ss_pred c-c--ceeecccchhhhhhCccCCCCceEEEEecCCccccHHHHHHcCCCeEEEEEEC
Q psy13245 76 S-P--RFDVPIRHIEKWTNNLLPSRQFGYVVLTTSGGIMDHEEARRKHLGGKILGFFF 130 (130)
Q Consensus 76 s-p--Rvy~~~~~i~~~~~~~~p~~~~Gi~IlSTskGimt~~eA~~~~vGGevL~~V~ 130 (130)
| | |+|+++++|+++.+| +|++|||||+||||++||+++++|||+||+||
T Consensus 81 SkPg~Rvy~~~~~L~~~~~g------~G~~IlSTskGimt~~eA~~~~iGGe~L~~v~ 132 (132)
T CHL00042 81 SKPGLRIYSNYKEIPRVLGG------MGIVILSTSKGIMTDREARLKGIGGEILCYIW 132 (132)
T ss_pred cCCCceeEcCHhHHHHHhCC------CcEEEEECCCCcccHHHHHHcCCCCEEEEEEC
Confidence 5 8 999999999999865 99999999999999999999999999999998
No 6
>PRK00136 rpsH 30S ribosomal protein S8; Validated
Probab=100.00 E-value=1.7e-44 Score=259.47 Aligned_cols=120 Identities=30% Similarity=0.501 Sum_probs=109.8
Q ss_pred ccchHHHHHHHhHhhhhhCCceEEEEeccchHHHHHHHHhhcCceeeEEEEcCCCCceEEEEeecccCcCccc------c
Q psy13245 3 RVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGYIGEFEIVDDHRAGKIVVNLKGRLNKCGVI------S 76 (130)
Q Consensus 3 ~~d~iad~lt~IrNa~~~~~~~~v~~p~sk~~~~il~iL~~eG~I~~~~~~~~~~~~~i~i~Lky~~~~~~~I------s 76 (130)
|+|+||||||+||||+++++.+| .+|+|+++++||++|++||||++|++.++++..+++|+|||+.+ .|+| |
T Consensus 2 ~~d~i~d~lt~IrNa~~~~~~~v-~ip~sk~~~~il~iL~~eGyI~~~~~~~~~~~~~~~v~Lky~~~-~pvi~~i~~IS 79 (130)
T PRK00136 2 MTDPIADMLTRIRNAQMAKHETV-SMPASKLKVAIAEILKEEGYIKDYEVEEDGKQGILRITLKYGEG-EPVIEGIKRVS 79 (130)
T ss_pred CcChHHHHHHHHHHHHHcCCCeE-EecccHHHHHHHHHHHHCCcccceEEEecCCcceEEEEEecCCC-CcccccceEec
Confidence 46999999999999999999995 69999999999999999999999998876556679999999865 4554 4
Q ss_pred -c--ceeecccchhhhhhCccCCCCceEEEEecCCccccHHHHHHcCCCeEEEEEEC
Q psy13245 77 -P--RFDVPIRHIEKWTNNLLPSRQFGYVVLTTSGGIMDHEEARRKHLGGKILGFFF 130 (130)
Q Consensus 77 -p--Rvy~~~~~i~~~~~~~~p~~~~Gi~IlSTskGimt~~eA~~~~vGGevL~~V~ 130 (130)
| |+|++.++|+++.+| +|++|+|||+|+|||+||+++++|||+||+||
T Consensus 80 kPg~Riy~~~~~l~~~~~g------~G~~IlSTs~Gimt~~eA~~~~iGGeiL~~v~ 130 (130)
T PRK00136 80 KPGLRVYKKKDELPKVLNG------LGIAIVSTSKGVMTDREARKAGVGGEVLCYVW 130 (130)
T ss_pred CCCcceEcCHhHHHHHHCC------CCEEEEEcCCCeeeHHHHHHhCCCCEEEEEEC
Confidence 7 999999999999865 99999999999999999999999999999998
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=3.5e-43 Score=252.03 Aligned_cols=119 Identities=41% Similarity=0.672 Sum_probs=107.8
Q ss_pred chHHHHHHHhHhhhhhCCceEEEEeccchHHHHHHHHhhcCceeeEEEEcCCCC-ceEEEEeecccCcCccc------c-
Q psy13245 5 NVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGYIGEFEIVDDHRA-GKIVVNLKGRLNKCGVI------S- 76 (130)
Q Consensus 5 d~iad~lt~IrNa~~~~~~~~v~~p~sk~~~~il~iL~~eG~I~~~~~~~~~~~-~~i~i~Lky~~~~~~~I------s- 76 (130)
|+|||+|++||||+++++.+ |.+|+|++++++|++|++||||++|++.+++++ ++++|+|||..++.++| |
T Consensus 1 D~lad~l~~I~Na~~~~~~~-v~ip~sk~~~~il~iL~~eGyI~~f~~~~~~~~~~~i~I~Lky~~~~~~~i~~i~~iSk 79 (129)
T PF00410_consen 1 DPLADLLTRIRNASRARKRF-VIIPYSKLNLSILKILKKEGYISGFEIIDDNRNGKRIWIELKYRRNGKPVIKKIKRISK 79 (129)
T ss_dssp SHHHHHHHHHHHHHHTTCSE-EEEEHCHHHHHHHHHHHHTTSEEEEEEEESSSSEEEEEEEESBCSSSSBSSSEEEESSB
T ss_pred CcHHHHHHHhHHHHHCCCCE-EEecccHHHHHHHHHHhhccccceeEeeccCCCceEEEEEEccccccchhhhhhhcccC
Confidence 89999999999999999999 478999999999999999999999999887765 57999999954444443 4
Q ss_pred c--ceeecccchhhhhhCccCCCCceEEEEecCCccccHHHHHHcCCCeEEEEEEC
Q psy13245 77 P--RFDVPIRHIEKWTNNLLPSRQFGYVVLTTSGGIMDHEEARRKHLGGKILGFFF 130 (130)
Q Consensus 77 p--Rvy~~~~~i~~~~~~~~p~~~~Gi~IlSTskGimt~~eA~~~~vGGevL~~V~ 130 (130)
| |+|++.+||+++.+| +|++|+|||+||||++||+++++|||+||+||
T Consensus 80 p~~r~y~~~~~L~~~~~g------~g~~IlSTskGImt~~eA~~~~vGGevL~~V~ 129 (129)
T PF00410_consen 80 PGRRVYISYKELPKVKNG------LGILILSTSKGIMTHREARKLNVGGEVLCYVW 129 (129)
T ss_dssp TTCCCEESGTGSHHSCTT------TSEEEEEETTEEEEHHHHHHHTSEEEEEEEEE
T ss_pred CCcceecCHHHHHHHhCC------CeEEEEEcCCCcEeHHHHHHcCCCCEEEEEEC
Confidence 5 999999999998754 99999999999999999999999999999998
No 8
>KOG1754|consensus
Probab=100.00 E-value=2.8e-38 Score=222.80 Aligned_cols=130 Identities=86% Similarity=1.381 Sum_probs=127.6
Q ss_pred CCccchHHHHHHHhHhhhhhCCceEEEEeccchHHHHHHHHhhcCceeeEEEEcCCCCceEEEEeecccCcCccccccee
Q psy13245 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGYIGEFEIVDDHRAGKIVVNLKGRLNKCGVISPRFD 80 (130)
Q Consensus 1 m~~~d~iad~lt~IrNa~~~~~~~~v~~p~sk~~~~il~iL~~eG~I~~~~~~~~~~~~~i~i~Lky~~~~~~~IspRvy 80 (130)
|++++.|||+|..|+||.+++|.+|.+-|.|+....+|.+|.++|||.+|++.+|++++++.|+|..|.|+|++||||+.
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 88999999999999999999999987789999999999999999999999999999999999999999999999999999
Q ss_pred ecccchhhhhhCccCCCCceEEEEecCCccccHHHHHHcCCCeEEEEEEC
Q psy13245 81 VPIRHIEKWTNNLLPSRQFGYVVLTTSGGIMDHEEARRKHLGGKILGFFF 130 (130)
Q Consensus 81 ~~~~~i~~~~~~~~p~~~~Gi~IlSTskGimt~~eA~~~~vGGevL~~V~ 130 (130)
++.++|++|.+..+|++++|+.+++||.|+|+|+||+.+++|||+||++|
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=66.99 E-value=4.6 Score=26.79 Aligned_cols=24 Identities=21% Similarity=0.362 Sum_probs=17.5
Q ss_pred chHHHHHHHHhhcCceeeEEEEcC
Q psy13245 32 KVIVKFLTVMMKHGYIGEFEIVDD 55 (130)
Q Consensus 32 k~~~~il~iL~~eG~I~~~~~~~~ 55 (130)
..-..++.-|.++|||+|+.+...
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 445578899999999999998643
No 10
>COG2519 GCD14 tRNA(1-methyladenosine) methyltransferase and related methyltransferases [Translation, ribosomal structure and biogenesis]
Probab=50.27 E-value=26 Score=28.06 Aligned_cols=42 Identities=19% Similarity=0.348 Sum_probs=37.3
Q ss_pred HHHHHHHhHhhhhhCCceEEEEeccchHHHHHHHHhhcCcee
Q psy13245 7 LSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGYIG 48 (130)
Q Consensus 7 iad~lt~IrNa~~~~~~~~v~~p~sk~~~~il~iL~~eG~I~ 48 (130)
..+++-++.++.+.+-..++.+|+.....+..+.|.+.||..
T Consensus 174 PW~~le~~~~~Lkpgg~~~~y~P~veQv~kt~~~l~~~g~~~ 215 (256)
T COG2519 174 PWNVLEHVSDALKPGGVVVVYSPTVEQVEKTVEALRERGFVD 215 (256)
T ss_pred hHHHHHHHHHHhCCCcEEEEEcCCHHHHHHHHHHHHhcCccc
Confidence 468889999999888888888999999999999999998864
No 11
>PHA02745 hypothetical protein; Provisional
Probab=38.40 E-value=28 Score=27.83 Aligned_cols=46 Identities=15% Similarity=0.234 Sum_probs=29.8
Q ss_pred cCceeeEEEEcCCCCceEEEEeecccCcCcccc--c--ceeecccchhhh
Q psy13245 44 HGYIGEFEIVDDHRAGKIVVNLKGRLNKCGVIS--P--RFDVPIRHIEKW 89 (130)
Q Consensus 44 eG~I~~~~~~~~~~~~~i~i~Lky~~~~~~~Is--p--Rvy~~~~~i~~~ 89 (130)
++=+..|..=++....--+=+||||.+.|+++- | .||+++.+|..-
T Consensus 120 ~~~~~~f~LPPeYDpnDsRWTLKyR~~~pGLVEL~P~SgVYV~~~~L~~C 169 (265)
T PHA02745 120 RQQIRKFTLPPEYDPNDSRWTLKHRYPGSGLVELLPHSGVYINAINLSNC 169 (265)
T ss_pred hccceeEecCCCCCCCCCcceeeccCCCCCcEEeecCCceEEeHHHHHHH
Confidence 444555544322212223557999999998886 7 799999887643
No 12
>PHA02943 hypothetical protein; Provisional
Probab=37.72 E-value=48 Score=24.81 Aligned_cols=21 Identities=24% Similarity=0.229 Sum_probs=17.8
Q ss_pred hHHHHHHHHhhcCceeeEEEE
Q psy13245 33 VIVKFLTVMMKHGYIGEFEIV 53 (130)
Q Consensus 33 ~~~~il~iL~~eG~I~~~~~~ 53 (130)
....+|.+|.+||+|+.++++
T Consensus 40 qa~~~LyvLErEG~VkrV~~G 60 (165)
T PHA02943 40 MARNALYQLAKEGMVLKVEIG 60 (165)
T ss_pred HHHHHHHHHHHcCceEEEeec
Confidence 456789999999999998864
No 13
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=35.94 E-value=71 Score=19.96 Aligned_cols=29 Identities=17% Similarity=0.271 Sum_probs=24.0
Q ss_pred EEEeccchHHHHHHHHhhcCceeeEEEEc
Q psy13245 26 LIRPCSKVIVKFLTVMMKHGYIGEFEIVD 54 (130)
Q Consensus 26 v~~p~sk~~~~il~iL~~eG~I~~~~~~~ 54 (130)
+.+.......++|+.|.++|+|.+|+...
T Consensus 45 i~l~~~~~~~~ll~~l~~~g~I~~f~~~~ 73 (84)
T PF13732_consen 45 IKLEDEETANELLQELIEKGIIRSFEEEE 73 (84)
T ss_pred EEECCcccHHHHHHHHHhCCCeeEEEEcC
Confidence 45666677789999999999999998754
No 14
>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=34.14 E-value=19 Score=26.56 Aligned_cols=16 Identities=38% Similarity=0.866 Sum_probs=13.9
Q ss_pred CceEEEEecCCccccH
Q psy13245 98 QFGYVVLTTSGGIMDH 113 (130)
Q Consensus 98 ~~Gi~IlSTskGimt~ 113 (130)
=+|..|+|||.||++.
T Consensus 106 y~GTTIvS~PGGIlDE 121 (153)
T PF09879_consen 106 YFGTTIVSHPGGILDE 121 (153)
T ss_pred cccceEecCCChhHHH
Confidence 3799999999999864
No 15
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=33.47 E-value=89 Score=20.05 Aligned_cols=18 Identities=22% Similarity=0.301 Sum_probs=13.7
Q ss_pred HHHHHHhhcCceeeEEEE
Q psy13245 36 KFLTVMMKHGYIGEFEIV 53 (130)
Q Consensus 36 ~il~iL~~eG~I~~~~~~ 53 (130)
.-++.|.++|||+.-...
T Consensus 33 ~hL~~Le~~GyV~~~k~~ 50 (80)
T PF13601_consen 33 KHLKKLEEAGYVEVEKEF 50 (80)
T ss_dssp HHHHHHHHTTSEEEEEE-
T ss_pred HHHHHHHHCCCEEEEEec
Confidence 446899999999986543
No 16
>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=29.31 E-value=1.5e+02 Score=19.53 Aligned_cols=26 Identities=12% Similarity=-0.010 Sum_probs=20.2
Q ss_pred eccchHHHHHHHHhhcCceeeEEEEc
Q psy13245 29 PCSKVIVKFLTVMMKHGYIGEFEIVD 54 (130)
Q Consensus 29 p~sk~~~~il~iL~~eG~I~~~~~~~ 54 (130)
+.......+|+-|.++|+|......+
T Consensus 37 i~~gtlY~~L~rLe~~GlI~~~~~~~ 62 (100)
T TIGR03433 37 VEEGSLYPALHRLERRGWIAAEWGES 62 (100)
T ss_pred cCCCcHHHHHHHHHHCCCeEEEeeec
Confidence 33456789999999999999975433
No 17
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=27.16 E-value=46 Score=18.89 Aligned_cols=14 Identities=14% Similarity=0.347 Sum_probs=10.9
Q ss_pred HHHHHHhhcCceee
Q psy13245 36 KFLTVMMKHGYIGE 49 (130)
Q Consensus 36 ~il~iL~~eG~I~~ 49 (130)
.=|+.|.+.|+|++
T Consensus 34 ~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 34 HHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHHHHTTSEEE
T ss_pred HHHHHHHHCcCeeC
Confidence 44688999999874
No 18
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=26.34 E-value=43 Score=21.29 Aligned_cols=43 Identities=21% Similarity=0.370 Sum_probs=26.3
Q ss_pred cchHHHHHHHhHhhhhhCCceEEEEeccch----HHHHHHHHhhcCceee
Q psy13245 4 VNVLSDALKSINNAEKRGKRQVLIRPCSKV----IVKFLTVMMKHGYIGE 49 (130)
Q Consensus 4 ~d~iad~lt~IrNa~~~~~~~~v~~p~sk~----~~~il~iL~~eG~I~~ 49 (130)
+|.++|+|..+.++.. .... ++-.+++ ....++-|.+.|+|+.
T Consensus 5 ~~Ii~~IL~~l~~~~~-~~t~--i~~~~~L~~~~~~~yL~~L~~~gLI~~ 51 (77)
T PF14947_consen 5 LEIIFDILKILSKGGA-KKTE--IMYKANLNYSTLKKYLKELEEKGLIKK 51 (77)
T ss_dssp THHHHHHHHHH-TT-B--HHH--HHTTST--HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHHHcCCC-CHHH--HHHHhCcCHHHHHHHHHHHHHCcCeeC
Confidence 4788999998865543 2333 1233333 3467889999999944
No 19
>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=26.21 E-value=76 Score=25.91 Aligned_cols=33 Identities=15% Similarity=0.274 Sum_probs=26.1
Q ss_pred CCceEEEE---eccchHHHHHHHHhhcCceeeEEEEc
Q psy13245 21 GKRQVLIR---PCSKVIVKFLTVMMKHGYIGEFEIVD 54 (130)
Q Consensus 21 ~~~~~v~~---p~sk~~~~il~iL~~eG~I~~~~~~~ 54 (130)
|++ ||.+ |.+.+...++.=|++.|||==....+
T Consensus 2 R~e-vVvI~Gs~~~PltR~la~DLeRRGFIV~v~~~~ 37 (299)
T PF08643_consen 2 RKE-VVVIAGSPHDPLTRSLALDLERRGFIVYVTVSS 37 (299)
T ss_pred cee-EEEEECCCCCccHHHHHHHHhhCCeEEEEEeCC
Confidence 444 4555 88999999999999999997776543
No 20
>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=25.34 E-value=79 Score=21.99 Aligned_cols=37 Identities=16% Similarity=0.221 Sum_probs=24.2
Q ss_pred HHHHHHhHhhhhhCCceEEEEeccchHHHHHHHHhhcCcee
Q psy13245 8 SDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGYIG 48 (130)
Q Consensus 8 ad~lt~IrNa~~~~~~~~v~~p~sk~~~~il~iL~~eG~I~ 48 (130)
.+.+.+|+..+ .... .+|.|-..+-.|+-+.++|||+
T Consensus 11 ~~ni~kl~~~~--~~~~--vVp~SA~aEl~Lr~a~k~g~I~ 47 (109)
T PF08438_consen 11 DENIEKLKEKY--PDEP--VVPTSAAAELALRKAAKAGLID 47 (109)
T ss_dssp HHHHHHHHHHH--TT-E--EEEE-HHHHHHHHS-SSS----
T ss_pred HhHHHHHHHhC--CCCc--eeeccHHHHHHHHHHHHCCCEE
Confidence 46778888866 2333 4799999999999999999998
No 21
>KOG3877|consensus
Probab=25.15 E-value=42 Score=27.86 Aligned_cols=41 Identities=37% Similarity=0.493 Sum_probs=28.9
Q ss_pred cchHHHHHHHhHhhhhhCCceEE-EEeccchHHHHHHHHhhcCceee
Q psy13245 4 VNVLSDALKSINNAEKRGKRQVL-IRPCSKVIVKFLTVMMKHGYIGE 49 (130)
Q Consensus 4 ~d~iad~lt~IrNa~~~~~~~~v-~~p~sk~~~~il~iL~~eG~I~~ 49 (130)
.|+-.|+|.||=|.- ...|. .-|+|.+ -+++.|.++|||..
T Consensus 157 ~~QY~dAL~HiL~TG---QGVVLERsp~SDF--VF~eAM~~qgyi~~ 198 (393)
T KOG3877|consen 157 FDQYLDALAHILNTG---QGVVLERSPHSDF--VFAEAMRDQGYIGH 198 (393)
T ss_pred HHHHHHHHHHHHhcC---CeEEEecCcchhH--HHHHHHHhcCcchh
Confidence 467778888887654 23211 2578877 57899999999976
No 22
>COG1244 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=23.68 E-value=1.3e+02 Score=25.36 Aligned_cols=41 Identities=22% Similarity=0.370 Sum_probs=28.5
Q ss_pred chHHHHHHHhHhhhhhCCceEEEEeccchHHHHHHHHhhcCc
Q psy13245 5 NVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGY 46 (130)
Q Consensus 5 d~iad~lt~IrNa~~~~~~~~v~~p~sk~~~~il~iL~~eG~ 46 (130)
+.|.|++..|+ |...+-..+-+.|.+-.+--+.+-|++.|.
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 46778888888 555566665556777667777777777764
No 23
>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=22.42 E-value=82 Score=20.82 Aligned_cols=36 Identities=14% Similarity=0.248 Sum_probs=28.2
Q ss_pred HHHhHhhhhhCCceEEEEeccchHHHHHHHHhhcCce
Q psy13245 11 LKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGYI 47 (130)
Q Consensus 11 lt~IrNa~~~~~~~~v~~p~sk~~~~il~iL~~eG~I 47 (130)
...|+++....... ...|......+.|.-|.+||.|
T Consensus 32 ~E~l~~~L~~~yp~-i~~Ps~e~l~~~L~~Li~erkI 67 (80)
T PF10264_consen 32 QETLREHLRKHYPG-IAIPSQEVLYNTLGTLIKERKI 67 (80)
T ss_pred HHHHHHHHHHhCCC-CCCCCHHHHHHHHHHHHHcCce
Confidence 34566666655565 4589999999999999999988
No 24
>KOG3467|consensus
Probab=22.12 E-value=1.4e+02 Score=20.28 Aligned_cols=32 Identities=22% Similarity=0.426 Sum_probs=21.7
Q ss_pred chHHHHHHHhHhhhhhCCceEEEEeccchHHHHHHHHhhcCc
Q psy13245 5 NVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGY 46 (130)
Q Consensus 5 d~iad~lt~IrNa~~~~~~~~v~~p~sk~~~~il~iL~~eG~ 46 (130)
|.|++.|+ |+..|+.+++ .+.+++..|+++|-
T Consensus 65 n~i~~A~~---yt~HAKRKTv-------T~~dvv~~LKR~G~ 96 (103)
T KOG3467|consen 65 NVIRDAVT---YTEHAKRKTV-------TAMDVVYALKRQGR 96 (103)
T ss_pred HHHHHHHH---HHhhhhhcee-------eHHHHHHHHHHcCc
Confidence 45555554 6666666653 46789999999983
No 25
>PRK00111 hypothetical protein; Provisional
Probab=21.83 E-value=81 Score=23.90 Aligned_cols=24 Identities=17% Similarity=0.260 Sum_probs=19.8
Q ss_pred CCccchHHHHHHHhHhhhhhCCce
Q psy13245 1 MVRVNVLSDALKSINNAEKRGKRQ 24 (130)
Q Consensus 1 m~~~d~iad~lt~IrNa~~~~~~~ 24 (130)
|.|.|+++++|.++|--.+.+.-.
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~ 24 (180)
T PRK00111 1 MTMTDPIEQAFERIRAEAMRRNGS 24 (180)
T ss_pred CCcccHHHHHHHHHHHHHhhccCC
Confidence 778899999999999877755554
No 26
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=21.40 E-value=91 Score=17.95 Aligned_cols=17 Identities=18% Similarity=0.645 Sum_probs=14.1
Q ss_pred hHHHHHHHHhhcCceee
Q psy13245 33 VIVKFLTVMMKHGYIGE 49 (130)
Q Consensus 33 ~~~~il~iL~~eG~I~~ 49 (130)
....+++-|.++||++.
T Consensus 34 tv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 34 TVHRLLQTLVEEGYVER 50 (52)
T ss_dssp HHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHHCcCeec
Confidence 45689999999999863
No 27
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=21.15 E-value=86 Score=19.91 Aligned_cols=20 Identities=25% Similarity=0.296 Sum_probs=16.4
Q ss_pred chHHHHHHHHhhcCceeeEE
Q psy13245 32 KVIVKFLTVMMKHGYIGEFE 51 (130)
Q Consensus 32 k~~~~il~iL~~eG~I~~~~ 51 (130)
....++++-|.++|+|++..
T Consensus 40 ~~l~kil~~L~~~Gli~s~~ 59 (83)
T PF02082_consen 40 SYLRKILQKLKKAGLIESSR 59 (83)
T ss_dssp HHHHHHHHHHHHTTSEEEET
T ss_pred HHHHHHHHHHhhCCeeEecC
Confidence 35678999999999998863
Done!