Query psy1555
Match_columns 271
No_of_seqs 70 out of 72
Neff 3.9
Searched_HMMs 46136
Date Sat Aug 17 00:09:44 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1555.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1555hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10245 MRP-S22: Mitochondria 100.0 2E-124 5E-129 847.4 23.5 243 11-256 1-243 (243)
2 KOG3890|consensus 100.0 1E-115 3E-120 813.2 17.7 258 4-264 32-291 (391)
3 PRK04081 hypothetical protein; 52.2 14 0.0003 34.1 2.9 40 101-143 59-98 (207)
4 PLN02940 riboflavin kinase 41.1 30 0.00065 33.5 3.6 39 45-83 336-374 (382)
5 PF01687 Flavokinase: Riboflav 33.9 34 0.00074 28.7 2.4 28 46-73 98-125 (125)
6 COG0488 Uup ATPase components 33.9 55 0.0012 33.7 4.3 41 86-127 319-359 (530)
7 PF06891 P2_Phage_GpR: P2 phag 33.7 23 0.0005 29.8 1.3 23 107-129 106-128 (135)
8 PRK14979 DNA-directed RNA poly 31.3 33 0.00073 31.0 2.0 33 97-129 131-163 (195)
9 KOG4070|consensus 29.9 23 0.00049 31.9 0.7 84 24-118 52-143 (180)
10 PF04571 Lipin_N: lipin, N-ter 29.6 25 0.00054 29.6 0.8 23 114-136 26-48 (110)
11 PF09282 Mago-bind: Mago bindi 26.3 28 0.00062 22.7 0.5 11 121-131 8-18 (27)
12 TIGR03209 P21_Cbot clostridium 23.3 1.1E+02 0.0024 24.4 3.6 60 170-231 7-66 (142)
13 cd06396 PB1_NBR1 The PB1 domai 22.6 95 0.0021 24.7 2.9 53 16-74 24-76 (81)
14 PF08838 DUF1811: Protein of u 21.9 76 0.0016 26.4 2.3 28 48-75 3-30 (102)
15 PRK12519 RNA polymerase sigma 20.3 1.8E+02 0.0039 24.4 4.4 60 170-231 37-96 (194)
No 1
>PF10245 MRP-S22: Mitochondrial 28S ribosomal protein S22; InterPro: IPR019374 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 [, ]. This is the conserved N terminus and central portion of the mitochondrial small subunit 28S ribosomal protein S22. Mammalian mitochondria carry out the synthesis of 13 polypeptides that are essential for oxidative phosphorylation and, hence, for the synthesis of the majority of the ATP used by eukaryotic organisms. The number of proteins produced by prokaryotes is smaller, reflected in the lower number of ribosomal proteins present in them [].
Probab=100.00 E-value=2.4e-124 Score=847.37 Aligned_cols=243 Identities=50% Similarity=0.820 Sum_probs=241.0
Q ss_pred CCCCCcHHHHHHHHHhhCCCchhhccccccCCCCCCCcccccCHHHHHHHHHHHHHHHHhhcCCCCcccccCCccccccc
Q psy1555 11 SALFFKPEVQELLLKLTRIDLSKVFRKQKYGQELKPPEYKFLTTEEVEKLKEEAYNRAIKKMQMPPIVPARDDSKLEVLS 90 (271)
Q Consensus 11 ~p~F~~~~VQ~LL~~lTgldl~KVFr~r~~g~~~~~p~yklMTdeql~~~~~~~~~~A~~~LqMPPVl~~R~~~~~~Vls 90 (271)
+|+|+|++||+||++|||+||+||||+| + +++++|+|||||||||++++++|+++|+++|||||||++|+| +++|||
T Consensus 1 ~p~F~~~~VQ~lL~~lT~~dl~KVFr~r-~-~~~~~p~yklMTdeql~~~~~~~~~~a~~~LqMPPVl~~r~~-~~~Vls 77 (243)
T PF10245_consen 1 QPLFTDEEVQNLLKKLTGLDLDKVFRPR-K-QELKPPTYKLMTDEQLEEALEKAIEKAKKLLQMPPVLEEREP-IDEVLS 77 (243)
T ss_pred CCCCccHHHHHHHHHHhCcCHHHhcccc-c-cCCCCCeeEeCCHHHHHHHHHHHHHHHHHhcCCCCCCCcccC-cccccc
Confidence 6999999999999999999999999999 4 688999999999999999999999999999999999999999 999999
Q ss_pred cCccccCCCccceEEEeccCCCCCCeeeEEEECCCCccccCChhHhhhhhhhccCCCCCccCCCCCCChhhHHHHHcchh
Q psy1555 91 NDKELLGHDVCKYVFTDITFGISDAKRIIVVREPDGLLREANTNERHRMNNIYFSRPGATYKHPDMFEEENLKALCDRKE 170 (271)
Q Consensus 91 ~D~~L~g~d~sk~VFTDIs~g~~~~eR~IVVREpdGtLR~A~~eERdRmnQiYFP~~gR~v~~P~mF~~e~L~~~l~~~~ 170 (271)
+||+|+|||+|||||||||||++|++|+|||||||||||+|||||||||||||||++||++++|+||+++||+++|++|+
T Consensus 78 ~D~~l~g~d~sk~VFTDIs~g~~~~eR~IVVREpdGtLR~At~eERdRm~QiYfP~~gR~v~~P~mF~~e~L~~~l~~~~ 157 (243)
T PF10245_consen 78 EDPALKGFDTSKYVFTDISYGIPHRERFIVVREPDGTLRKATWEERDRMNQIYFPKEGRKVRPPPMFEDENLQNLLDRDR 157 (243)
T ss_pred cCccccCCCcceEEEEecccCCCCccceEEEECCCCCcccCCHHHHHhHHhhccCCCCCccCCCCccCcHHHHHHHhccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHhhcCCCchhhhHHHHHHhhhhhhhcCccccccCCCchhHHHHHHHcCChhHHHHHHHhhchHHhHHHHHHH
Q psy1555 171 YVFILDRAATQYEPDDQLYHNILNTTFTHIHENNGFDHLRSTRHFGCLVFFLANNNIIDNLLLQNLHCNMIEDAVWLIKV 250 (271)
Q Consensus 171 ~e~iLD~ac~QfEPdd~~Y~rv~~~vYe~i~~~~~fd~LrSTRHFG~mafyL~~~~~id~LL~d~i~~~~l~dA~~Li~L 250 (271)
|||||||||+|||||||+||+||++||+|||++|+||+||||||||||||||||+++|||||++||++++|+||++||+|
T Consensus 158 ~e~iLD~ac~QfEPdd~~y~rv~~~vYe~i~~~~~yd~LrSTRHfG~m~fyL~~~~~id~LL~dmi~~~~l~dA~~Li~L 237 (243)
T PF10245_consen 158 HEFILDRACVQFEPDDPDYIRVHHRVYEHINEHKKYDLLRSTRHFGPMAFYLVWNKKIDGLLYDMIQRDRLDDAVNLIRL 237 (243)
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHhccccHHHhccCccchhHHHHHHccCcHHHHHHHHHhhHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHcC
Q psy1555 251 YQIVNP 256 (271)
Q Consensus 251 ~~~lhp 256 (271)
||+|||
T Consensus 238 ~~~lhP 243 (243)
T PF10245_consen 238 YHMLHP 243 (243)
T ss_pred hhhcCC
Confidence 999999
No 2
>KOG3890|consensus
Probab=100.00 E-value=1.4e-115 Score=813.20 Aligned_cols=258 Identities=41% Similarity=0.625 Sum_probs=253.6
Q ss_pred cccCCCCCCCCCcHHHHHHHHHhhCCCchhhccccccCCCCCCCcccccCHHHHHHHHHHHHHHHHhhcCCCCcccccCC
Q psy1555 4 KTITKSTSALFFKPEVQELLLKLTRIDLSKVFRKQKYGQELKPPEYKFLTTEEVEKLKEEAYNRAIKKMQMPPIVPARDD 83 (271)
Q Consensus 4 ~~~~~d~~p~F~~~~VQ~LL~~lTgldl~KVFr~r~~g~~~~~p~yklMTdeql~~~~~~~~~~A~~~LqMPPVl~~R~~ 83 (271)
-+|+.||+|+|+|+|||+||++|||+||+|||||| + +++++|+|||||.|||+++.+++.++|+++||||||+++|+|
T Consensus 32 ~~~~~~~~plF~d~EvQ~lLt~mT~lnL~Kvfrpr-~-~~~~~~~~klMt~eqLe~~~~~~ve~A~~~LqmpPV~e~r~~ 109 (391)
T KOG3890|consen 32 LQYERDPQPLFTDAEVQRLLTSMTQLNLDKVFRPR-T-VPDNSSETKLMTNEQLENEFQNLVERAQQILQMPPVVEIRKD 109 (391)
T ss_pred cCCCCCccccchHHHHHHHHHHhhhccHHhhcccc-c-ccCCCchhhhhhHHHHHHHHHHHHHHHHHHhcCCCcccccch
Confidence 47899999999999999999999999999999999 6 799999999999999999999999999999999999999999
Q ss_pred ccccccccCccccCCCccceEEEeccCCCCCCeeeEEEECCCCccccCChhHhhhhhhhccCCCCCccCCCCCCChhhHH
Q psy1555 84 SKLEVLSNDKELLGHDVCKYVFTDITFGISDAKRIIVVREPDGLLREANTNERHRMNNIYFSRPGATYKHPDMFEEENLK 163 (271)
Q Consensus 84 ~~~~Vls~D~~L~g~d~sk~VFTDIs~g~~~~eR~IVVREpdGtLR~A~~eERdRmnQiYFP~~gR~v~~P~mF~~e~L~ 163 (271)
+++|||+|.+|+||+||||||||||||+++++|+|||||||||||+|||||+|||||+|||++||++++|+||.||||+
T Consensus 110 -v~~vlAkD~~Lkdf~tsKfVFTDItf~~~~~eR~VVVRepdGTLr~A~~ee~dRMnq~YfpkegR~~~tP~~F~eenL~ 188 (391)
T KOG3890|consen 110 -VERVLAKDTALKDFATSKFVFTDITFGRRQSERKVVVREPDGTLRYATLEETDRMNQLYFPKEGRQSYTPRMFAEENLA 188 (391)
T ss_pred -HHHHHhhhhhhccccccceEEEeecccCccccceEEEECCCCccccCCHHHhhhhhhhcccCCCCccCCCccccchHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHcchhhHHHHHHHHhhcCCCchhhhHHHHHHhhhhhhhcCccccccCCCchhHHHHHHHcCChhHHHHHHHhhchHHh
Q psy1555 164 ALCDRKEYVFILDRAATQYEPDDQLYHNILNTTFTHIHENNGFDHLRSTRHFGCLVFFLANNNIIDNLLLQNLHCNMIED 243 (271)
Q Consensus 164 ~~l~~~~~e~iLD~ac~QfEPdd~~Y~rv~~~vYe~i~~~~~fd~LrSTRHFG~mafyL~~~~~id~LL~d~i~~~~l~d 243 (271)
+||++++|||||||||||||||||+||+|+++||||||++|+||+||||||||||+||+|||+|||+||+|||++|+|+|
T Consensus 189 ~~l~~~~hefVLd~~~~qyEPd~pey~~is~~vfe~inesgkfdllrSTRhFGpm~fy~a~n~~Id~LL~d~i~rd~l~d 268 (391)
T KOG3890|consen 189 KCLAEHKHEFVLDRLLVQYEPDEPEYHNISARVFEHINESGKFDLLRSTRHFGPMAFYYAWNRCIDDLLYDMIRRDYLHD 268 (391)
T ss_pred HHHhhcchHHHHHHHHHhcCCCChHHhhhHHHHHHhhccccceeeEeeccccCceeeeeehhhhHHHHHHHHhhhhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHcCCCch--hhHh
Q psy1555 244 AVWLIKVYQIVNPESKC--ATVE 264 (271)
Q Consensus 244 A~~Li~L~~~lhp~~~~--a~~~ 264 (271)
|++||+|||.+||++.+ |+-+
T Consensus 269 a~nLV~L~~~lhpd~~~~~Aqg~ 291 (391)
T KOG3890|consen 269 AVNLVALSYKLHPDPVEYQAQGT 291 (391)
T ss_pred HHHHHHHHHHhCCcchhhhhccc
Confidence 99999999999999998 5444
No 3
>PRK04081 hypothetical protein; Provisional
Probab=52.17 E-value=14 Score=34.14 Aligned_cols=40 Identities=18% Similarity=0.231 Sum_probs=30.9
Q ss_pred cceEEEeccCCCCCCeeeEEEECCCCccccCChhHhhhhhhhc
Q psy1555 101 CKYVFTDITFGISDAKRIIVVREPDGLLREANTNERHRMNNIY 143 (271)
Q Consensus 101 sk~VFTDIs~g~~~~eR~IVVREpdGtLR~A~~eERdRmnQiY 143 (271)
-+|..+|= .|-.+=.||||++||+=|..+.||=|+++..=
T Consensus 59 G~YKI~eE---~Ps~~Trvilr~~dG~ER~LS~eE~dkLi~eE 98 (207)
T PRK04081 59 GSYKILEE---YPSSETRVVLRDLDGTERVLSQEEIDKLIKEE 98 (207)
T ss_pred CceEeeee---cCCCcceEEEecCCCcccccCHHHHHHHHHHH
Confidence 34554442 25556779999999999999999999998753
No 4
>PLN02940 riboflavin kinase
Probab=41.10 E-value=30 Score=33.51 Aligned_cols=39 Identities=26% Similarity=0.282 Sum_probs=35.3
Q ss_pred CCCcccccCHHHHHHHHHHHHHHHHhhcCCCCcccccCC
Q psy1555 45 KPPEYKFLTTEEVEKLKEEAYNRAIKKMQMPPIVPARDD 83 (271)
Q Consensus 45 ~~p~yklMTdeql~~~~~~~~~~A~~~LqMPPVl~~R~~ 83 (271)
=+|+.||-+-++|.+.+.+-++.|++.|.+||-..-+++
T Consensus 336 lR~e~kF~~~~~L~~qi~~D~~~a~~~~~~~~~~~~~~~ 374 (382)
T PLN02940 336 IRPEANFPSLESLIAKIHEDRRIAEKALDLPLYAKYKDD 374 (382)
T ss_pred cCCCCCCCCHHHHHHHHHHHHHHHHHHHcCchhhhhccC
Confidence 478899999999999999999999999999998776665
No 5
>PF01687 Flavokinase: Riboflavin kinase; InterPro: IPR015865 Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (2.7.1.26 from EC), which converts it into FMN, and FAD synthetase (2.7.7.2 from EC), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme [], the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family []. The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases []. This entry represents the riboflavin kinase domains from bacteria and eukaryotes.; GO: 0008531 riboflavin kinase activity, 0009231 riboflavin biosynthetic process; PDB: 1Q9S_A 1NB9_A 1P4M_A 1NB0_A 3OP1_B 1T6Z_A 2I1L_A 1T6Y_B 1T6X_B 1S4M_A ....
Probab=33.94 E-value=34 Score=28.68 Aligned_cols=28 Identities=32% Similarity=0.391 Sum_probs=21.8
Q ss_pred CCcccccCHHHHHHHHHHHHHHHHhhcC
Q psy1555 46 PPEYKFLTTEEVEKLKEEAYNRAIKKMQ 73 (271)
Q Consensus 46 ~p~yklMTdeql~~~~~~~~~~A~~~Lq 73 (271)
+|+-||-+-++|.+++.+-++.|++.||
T Consensus 98 R~e~kF~s~e~L~~qI~~D~~~a~~~lq 125 (125)
T PF01687_consen 98 RPEKKFDSLEELKEQIKKDIEQARKYLQ 125 (125)
T ss_dssp EE----SSHHHHHHHHHHHHHHHHHHH-
T ss_pred cCCcccCCHHHHHHHHHHHHHHHHHhcC
Confidence 5677999999999999999999999998
No 6
>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]
Probab=33.89 E-value=55 Score=33.72 Aligned_cols=41 Identities=29% Similarity=0.460 Sum_probs=34.2
Q ss_pred ccccccCccccCCCccceEEEeccCCCCCCeeeEEEECCCCc
Q psy1555 86 LEVLSNDKELLGHDVCKYVFTDITFGISDAKRIIVVREPDGL 127 (271)
Q Consensus 86 ~~Vls~D~~L~g~d~sk~VFTDIs~g~~~~eR~IVVREpdGt 127 (271)
..|+.-+..-.||+..+.||.|+||++..-+|..+| -|||.
T Consensus 319 ~~vl~~~~~~~~y~~~~~l~~~~s~~i~~g~riaii-G~NG~ 359 (530)
T COG0488 319 KLVLEFENVSKGYDGGRLLLKDLSFRIDRGDRIAIV-GPNGA 359 (530)
T ss_pred CeeEEEeccccccCCCceeecCceEEecCCCEEEEE-CCCCC
Confidence 568888888889988899999999999999986665 46663
No 7
>PF06891 P2_Phage_GpR: P2 phage tail completion protein R (GpR); InterPro: IPR009678 This family consists of P2 phage tail completion protein R (GpR) and similar sequences from related phage. GpR is thought to be a tail completion protein which is essential for stable head joining []. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=33.69 E-value=23 Score=29.81 Aligned_cols=23 Identities=26% Similarity=0.605 Sum_probs=21.4
Q ss_pred eccCCCCCCeeeEEEECCCCccc
Q psy1555 107 DITFGISDAKRIIVVREPDGLLR 129 (271)
Q Consensus 107 DIs~g~~~~eR~IVVREpdGtLR 129 (271)
||++.++=.||.+|+.+++|.+-
T Consensus 106 dl~i~l~ltE~v~v~~~~~G~i~ 128 (135)
T PF06891_consen 106 DLSITLPLTERVIVIEDEDGPIP 128 (135)
T ss_pred EEEEEEeeEEEEEEEECCCCCEE
Confidence 99999999999999999999864
No 8
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=31.31 E-value=33 Score=31.04 Aligned_cols=33 Identities=12% Similarity=0.103 Sum_probs=31.3
Q ss_pred CCCccceEEEeccCCCCCCeeeEEEECCCCccc
Q psy1555 97 GHDVCKYVFTDITFGISDAKRIIVVREPDGLLR 129 (271)
Q Consensus 97 g~d~sk~VFTDIs~g~~~~eR~IVVREpdGtLR 129 (271)
|+..|||.=+|-.|...+.+|++.--|+||++.
T Consensus 131 Gy~hAk~~pvda~y~~~~~dkl~leIeTdGsi~ 163 (195)
T PRK14979 131 GKIHAKWQPCNAVYKQISNDEVEFKVESFGQMD 163 (195)
T ss_pred ccccccccceeeEEecCCCcEEEEEEEECCCCC
Confidence 899999999999999999999999999999985
No 9
>KOG4070|consensus
Probab=29.92 E-value=23 Score=31.85 Aligned_cols=84 Identities=26% Similarity=0.251 Sum_probs=51.2
Q ss_pred HHhhCCCchhhccccccCCCCCCCcccccCHHHHHHHHHHHH-HHHHhhcCCCCcccccCCcccc-ccccCccccCCCcc
Q psy1555 24 LKLTRIDLSKVFRKQKYGQELKPPEYKFLTTEEVEKLKEEAY-NRAIKKMQMPPIVPARDDSKLE-VLSNDKELLGHDVC 101 (271)
Q Consensus 24 ~~lTgldl~KVFr~r~~g~~~~~p~yklMTdeql~~~~~~~~-~~A~~~LqMPPVl~~R~~~~~~-Vls~D~~L~g~d~s 101 (271)
+.+|+.|..=||++. +|.. ....|=+|.++++++-. .+++.+ |.-++=.+ |.+ +-.++|+..|-.-+
T Consensus 52 K~vT~tdt~i~fsKv-kg~~-----~~~~tf~~fkkal~ela~~R~k~K----s~ee~l~~-I~~llagkaP~~~gvtka 120 (180)
T KOG4070|consen 52 KSVTGTDTDIVFSKV-KGKK-----ARTITFEEFKKALEELATKRFKGK----SKEEALDA-ICQLLAGKAPAVVGVTKA 120 (180)
T ss_pred Ccccccccceeeeec-cccc-----cccccHHHHHHHHHHHHHhhhcCC----CHHHHHHH-HHHHHhccCCcccchhhc
Confidence 468899999999888 5433 33456678888777543 333332 32222233 555 44578888776544
Q ss_pred ce-----EEEecc-CCCCCCeee
Q psy1555 102 KY-----VFTDIT-FGISDAKRI 118 (271)
Q Consensus 102 k~-----VFTDIs-~g~~~~eR~ 118 (271)
|= =.||.| |-=+|+|||
T Consensus 121 ~t~gavdRLTDtskyTGsHKErF 143 (180)
T KOG4070|consen 121 KTAGAVDRLTDTSKYTGSHKERF 143 (180)
T ss_pred cccccccccccccccccchhhhc
Confidence 42 256666 556788887
No 10
>PF04571 Lipin_N: lipin, N-terminal conserved region; InterPro: IPR007651 Mutations in the lipin gene lead to fatty liver dystrophy in mice. The protein has been shown to be phosphorylated by the TOR Ser/Thr protein kinases in response to insulin stimulation. This entry represents a conserved domain found at the N terminus of the member proteins [, ].
Probab=29.60 E-value=25 Score=29.58 Aligned_cols=23 Identities=39% Similarity=0.606 Sum_probs=18.8
Q ss_pred CCeeeEEEECCCCccccCChhHh
Q psy1555 114 DAKRIIVVREPDGLLREANTNER 136 (271)
Q Consensus 114 ~~eR~IVVREpdGtLR~A~~eER 136 (271)
---=.|||+-|||+|+.-.|--|
T Consensus 26 GAiDVIVV~q~DGs~~sSPFhVR 48 (110)
T PF04571_consen 26 GAIDVIVVEQPDGSLKSSPFHVR 48 (110)
T ss_pred CceeEEEEecCCCCEecCccEEE
Confidence 34457999999999999998755
No 11
>PF09282 Mago-bind: Mago binding; InterPro: IPR015362 Members of this family adopt a structure consisting of a small globular all-beta-domain, with a three-stranded beta-sheet and a contiguous beta-hairpin. They bind to Mago alpha-helices via extensive electrostatic interactions and at a beta2-beta3 loop via hydrophobic interactions []. ; GO: 0005515 protein binding; PDB: 1RK8_C.
Probab=26.26 E-value=28 Score=22.66 Aligned_cols=11 Identities=36% Similarity=0.718 Sum_probs=5.8
Q ss_pred EECCCCccccC
Q psy1555 121 VREPDGLLREA 131 (271)
Q Consensus 121 VREpdGtLR~A 131 (271)
-+-||||+|++
T Consensus 8 s~RpDGt~RK~ 18 (27)
T PF09282_consen 8 SQRPDGTWRKE 18 (27)
T ss_dssp EE-TTS-EE--
T ss_pred ccCCCCCcccc
Confidence 36799999985
No 12
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=23.30 E-value=1.1e+02 Score=24.43 Aligned_cols=60 Identities=10% Similarity=0.142 Sum_probs=39.6
Q ss_pred hhHHHHHHHHhhcCCCchhhhHHHHHHhhhhhhhcCccccccCCCchhHHHHHHHcCChhHH
Q psy1555 170 EYVFILDRAATQYEPDDQLYHNILNTTFTHIHENNGFDHLRSTRHFGCLVFFLANNNIIDNL 231 (271)
Q Consensus 170 ~~e~iLD~ac~QfEPdd~~Y~rv~~~vYe~i~~~~~fd~LrSTRHFG~mafyL~~~~~id~L 231 (271)
.|--+|-+.|..|.-++ +.+.|...+|.++... .-+.++....|.+..|=.+.|.++|-+
T Consensus 7 ~y~~~l~~~~~~~~~~~-~~qdvf~~~w~~~~~~-~~~~~~~~~~~~~wL~~iarN~~id~~ 66 (142)
T TIGR03209 7 NFKNTIDIFTRKYNLYY-DYNDILYHLWIILKKI-DLNKFNTENDLEKYISTSLKRYCLDIC 66 (142)
T ss_pred HHHHHHHHHHHHhcchh-hHHHHHHHHHHHHHHh-hhhhcCchhHHHHHHHHHHHHHHHHHH
Confidence 45556667777776666 5699999999986643 212234445576666666788877765
No 13
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=22.57 E-value=95 Score=24.65 Aligned_cols=53 Identities=17% Similarity=0.132 Sum_probs=38.0
Q ss_pred cHHHHHHHHHhhCCCchhhccccccCCCCCCCcccccCHHHHHHHHHHHHHHHHhhcCC
Q psy1555 16 KPEVQELLLKLTRIDLSKVFRKQKYGQELKPPEYKFLTTEEVEKLKEEAYNRAIKKMQM 74 (271)
Q Consensus 16 ~~~VQ~LL~~lTgldl~KVFr~r~~g~~~~~p~yklMTdeql~~~~~~~~~~A~~~LqM 74 (271)
=++++.-+.++.+++ -| .-|. --...-...+.++++|+|+++-+.. --+.|||
T Consensus 24 ~~~L~~ev~~rf~l~---~f-~lKY-lDde~e~v~lssd~eLeE~~rl~~~-~~~~l~~ 76 (81)
T cd06396 24 WASVEAMVKVSFGLN---DI-QIKY-VDEENEEVSVNSQGEYEEALKSAVR-QGNLLQM 76 (81)
T ss_pred HHHHHHHHHHHhCCC---cc-eeEE-EcCCCCEEEEEchhhHHHHHHHHHh-CCCEEEE
Confidence 367888888888888 56 2334 3455566789999999999995544 4466776
No 14
>PF08838 DUF1811: Protein of unknown function (DUF1811); InterPro: IPR014938 This entry consists uncharacterised bacterial proteins. Some of the proteins are annotated as being transcriptional regulators (see Q4MQL7 from SWISSPROT, Q65MA2 from SWISSPROT). The structure of one of the proteins has revealed a beta-barrel like structure with helix-turn-helix like motif. ; PDB: 2YXY_A 1SF9_A.
Probab=21.91 E-value=76 Score=26.44 Aligned_cols=28 Identities=21% Similarity=0.240 Sum_probs=21.7
Q ss_pred cccccCHHHHHHHHHHHHHHHHhhcCCC
Q psy1555 48 EYKFLTTEEVEKLKEEAYNRAIKKMQMP 75 (271)
Q Consensus 48 ~yklMTdeql~~~~~~~~~~A~~~LqMP 75 (271)
.|--||.+||+.+++.-.++|++.=||=
T Consensus 3 rySeMs~~EL~~Ei~~L~ekarKAEq~G 30 (102)
T PF08838_consen 3 RYSEMSEEELRQEIARLKEKARKAEQLG 30 (102)
T ss_dssp HHHC--HHHHHHHHHHHHHHHHHHHHCT
T ss_pred chhhcCHHHHHHHHHHHHHHHHHHHHcC
Confidence 3667999999999999999998876653
No 15
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=20.28 E-value=1.8e+02 Score=24.41 Aligned_cols=60 Identities=15% Similarity=0.208 Sum_probs=45.4
Q ss_pred hhHHHHHHHHhhcCCCchhhhHHHHHHhhhhhhhcCccccccCCCchhHHHHHHHcCChhHH
Q psy1555 170 EYVFILDRAATQYEPDDQLYHNILNTTFTHIHENNGFDHLRSTRHFGCLVFFLANNNIIDNL 231 (271)
Q Consensus 170 ~~e~iLD~ac~QfEPdd~~Y~rv~~~vYe~i~~~~~fd~LrSTRHFG~mafyL~~~~~id~L 231 (271)
+|.-.|-+.|..+-.+..+-.-|.+.||-.+-....|+.-. .+|++.++=.+.|..+|-+
T Consensus 37 ~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~ 96 (194)
T PRK12519 37 RHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSSYDPKR--GSLSSYLLTLTRSRAIDRL 96 (194)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCccc--ccHHHHHHHHHHHHHHHHH
Confidence 45666777888888888888889999998887665565433 3699988888887777765
Done!