Query 031427
Match_columns 160
No_of_seqs 117 out of 1089
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 13:57:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031427.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031427hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05591 rplQ 50S ribosomal pr 100.0 3.7E-55 8.1E-60 332.6 14.2 113 1-113 1-113 (113)
2 TIGR00059 L17 ribosomal protei 100.0 5.2E-55 1.1E-59 331.4 14.1 112 3-114 1-112 (112)
3 COG0203 RplQ Ribosomal protein 100.0 4.8E-55 1E-59 332.4 13.0 112 2-113 5-116 (116)
4 PTZ00076 60S ribosomal protein 100.0 1.4E-51 2.9E-56 346.4 14.5 128 3-130 18-146 (253)
5 KOG3280 Mitochondrial/chloropl 100.0 2.9E-51 6.2E-56 327.8 11.2 150 5-158 15-167 (171)
6 PF01196 Ribosomal_L17: Riboso 100.0 3.4E-48 7.3E-53 287.3 10.5 97 17-113 1-97 (97)
7 PRK13266 Thf1-like protein; Re 45.8 35 0.00075 29.2 4.2 78 9-98 68-147 (225)
8 COG1775 HgdB Benzoyl-CoA reduc 42.6 49 0.0011 30.5 4.9 89 26-114 160-259 (379)
9 PF02082 Rrf2: Transcriptional 38.6 69 0.0015 22.0 4.2 47 46-92 12-66 (83)
10 PRK13848 conjugal transfer pro 36.4 36 0.00079 25.7 2.6 24 69-92 45-68 (98)
11 PF05848 CtsR: Firmicute trans 32.5 5.2 0.00011 32.2 -2.6 71 43-116 10-92 (152)
12 PLN00047 photosystem II biogen 27.4 1.3E+02 0.0028 26.7 4.9 78 9-98 119-197 (283)
13 KOG0111 Cyclophilin-type pepti 26.4 45 0.00097 29.3 1.9 46 111-156 76-129 (298)
14 PF05598 DUF772: Transposase d 25.3 2.1E+02 0.0046 18.9 5.9 72 8-81 1-77 (77)
15 PF04079 DUF387: Putative tran 24.8 1.5E+02 0.0033 23.6 4.5 46 45-92 3-48 (159)
16 PRK00135 scpB segregation and 24.7 2.2E+02 0.0047 23.3 5.6 51 41-91 5-55 (188)
17 COG4463 CtsR Transcriptional r 22.8 49 0.0011 26.8 1.4 13 88-100 64-76 (153)
18 cd00491 4Oxalocrotonate_Tautom 21.0 1.2E+02 0.0026 18.9 2.7 21 8-28 10-30 (58)
19 COG2257 Uncharacterized homolo 20.9 83 0.0018 23.6 2.2 42 43-84 32-79 (92)
20 COG5095 TAF6 Transcription ini 20.2 1.3E+02 0.0028 27.7 3.7 40 38-77 192-232 (450)
21 PF07820 TraC: TraC-like prote 20.0 99 0.0021 23.2 2.4 21 69-89 44-64 (92)
No 1
>PRK05591 rplQ 50S ribosomal protein L17; Validated
Probab=100.00 E-value=3.7e-55 Score=332.56 Aligned_cols=113 Identities=52% Similarity=0.827 Sum_probs=111.6
Q ss_pred CCcccCCCCCchHHHHHHHHHHHHHHhccceeecHHhHHHHHhhHHHHHHhhccCChHHHHHHHHhccChhHHHHHHHHH
Q 031427 1 MTKFRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTEL 80 (160)
Q Consensus 1 m~~~rklgr~~~hR~allRnlvtsLi~herI~TT~~KAKelr~~aEkLIt~AK~g~~~~~r~a~~~L~~~~~v~KLF~~l 80 (160)
|++++||||+++||++|||||+||||+||+|+||++||||+|+|||+|||+||+|++|++|+|.+||.|+++++|||++|
T Consensus 1 ~~~~rkl~r~~~hR~allrnl~tsLi~herI~TT~~KAKelr~~aEklIt~aK~~~~~~rR~~~~~L~~~~~v~KLf~~l 80 (113)
T PRK05591 1 RKKGRKLGRTSSHRKAMLRNLATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLHARRQAFARLRDKEAVHKLFDEI 80 (113)
T ss_pred CCCCCCCCCChHHHHHHHHHHHHHHHHcCeEEecHHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHhCCHHHHHHHHHHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhCCCCCCeeEEEcccCCCCCCCCeeeeEec
Q 031427 81 AYRYKDRAGGYTRLLRSRIRVGDAAPMAYIEFV 113 (160)
Q Consensus 81 apRy~~R~GGYTRI~kl~~R~GD~ApmaiIElV 113 (160)
+|||++|+||||||+|+++|.||+|||||||||
T Consensus 81 apry~~R~GGYTRI~k~~~R~gD~A~ma~iElV 113 (113)
T PRK05591 81 APRYADRNGGYTRILKLGFRRGDNAPMAIIELV 113 (113)
T ss_pred HHHhCcCCCCeEEEEECCCCCCCCCCeEEEEeC
Confidence 999999999999999999999999999999997
No 2
>TIGR00059 L17 ribosomal protein L17. Eubacterial and mitochondrial. The mitochondrial form, from yeast, contains an additional 110 amino acids C-terminal to the region found by this model.
Probab=100.00 E-value=5.2e-55 Score=331.38 Aligned_cols=112 Identities=48% Similarity=0.835 Sum_probs=110.4
Q ss_pred cccCCCCCchHHHHHHHHHHHHHHhccceeecHHhHHHHHhhHHHHHHhhccCChHHHHHHHHhccChhHHHHHHHHHHH
Q 031427 3 KFRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAY 82 (160)
Q Consensus 3 ~~rklgr~~~hR~allRnlvtsLi~herI~TT~~KAKelr~~aEkLIt~AK~g~~~~~r~a~~~L~~~~~v~KLF~~lap 82 (160)
.++||||+++||++|||||+||||+||+|+||++||||+|+|||+|||+||+|++|++|+|.+||.|+++++|||++|+|
T Consensus 1 ~~~klgr~~~hR~allrnl~tsLi~herI~TT~~KAKelr~~aEklIt~AK~~~~~~rR~~~~~l~~~~~v~KLf~~lap 80 (112)
T TIGR00059 1 SYRKLGRTSAHRKALLRNLASALIRHEKIKTTLAKAKELRRVVEKLITLAKVDNFNNRREAKAYIRNKEIVHKLFSEIAP 80 (112)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHCCeEEECHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhCCCCCCeeEEEcccCCCCCCCCeeeeEecc
Q 031427 83 RYKDRAGGYTRLLRSRIRVGDAAPMAYIEFVD 114 (160)
Q Consensus 83 Ry~~R~GGYTRI~kl~~R~GD~ApmaiIElVd 114 (160)
||++|+||||||+|+++|.||+||||||||||
T Consensus 81 ry~~R~GGYTRI~kl~~R~gD~A~maiiElVd 112 (112)
T TIGR00059 81 RYAQRPGGYTRILKLGPRRGDAAEMAIIELVD 112 (112)
T ss_pred HhCCCCCCeEEEEECCCCCCCCCCeEEEEecC
Confidence 99999999999999999999999999999996
No 3
>COG0203 RplQ Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.8e-55 Score=332.35 Aligned_cols=112 Identities=51% Similarity=0.810 Sum_probs=110.7
Q ss_pred CcccCCCCCchHHHHHHHHHHHHHHhccceeecHHhHHHHHhhHHHHHHhhccCChHHHHHHHHhccChhHHHHHHHHHH
Q 031427 2 TKFRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELA 81 (160)
Q Consensus 2 ~~~rklgr~~~hR~allRnlvtsLi~herI~TT~~KAKelr~~aEkLIt~AK~g~~~~~r~a~~~L~~~~~v~KLF~~la 81 (160)
++++||||+++||++|||||++|||.||+|+||++||||+|+++|+|||+||.|+++++|+|.++|.|+++++|||++|+
T Consensus 5 ~~~rkl~rtsshR~amlrnla~sLi~he~I~TT~~KAKelr~~vEkLITlaK~~~l~~RR~a~~~l~d~~~v~kLF~~ia 84 (116)
T COG0203 5 KKGRKLGRTSSHRKAMLRNLATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLANRRLAFARLRDKDAVKKLFDEIA 84 (116)
T ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHcCceeecHHHHHHHHHHHHHHHHHhhcccHHHHHHHHHHcccHHHHHHHHHHhC
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhCCCCCCeeEEEcccCCCCCCCCeeeeEec
Q 031427 82 YRYKDRAGGYTRLLRSRIRVGDAAPMAYIEFV 113 (160)
Q Consensus 82 pRy~~R~GGYTRI~kl~~R~GD~ApmaiIElV 113 (160)
|||.+|+||||||+|+|+|.||+|||||||||
T Consensus 85 pry~~R~GGYtRIlK~g~R~GD~A~maiiElV 116 (116)
T COG0203 85 PRYAERNGGYTRILKLGFRRGDNAPMAIIELV 116 (116)
T ss_pred hhhcCCCCCeeEEEecCCCCCCCCceEEEEeC
Confidence 99999999999999999999999999999997
No 4
>PTZ00076 60S ribosomal protein L17; Provisional
Probab=100.00 E-value=1.4e-51 Score=346.42 Aligned_cols=128 Identities=32% Similarity=0.532 Sum_probs=123.9
Q ss_pred cccCCCCCchHHHHHHHHHHHHHHhccceeecHHhHHHHHhhHHHHHHhhccCChHHHHHHHHhccChhHHHHHHHHHHH
Q 031427 3 KFRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAY 82 (160)
Q Consensus 3 ~~rklgr~~~hR~allRnlvtsLi~herI~TT~~KAKelr~~aEkLIt~AK~g~~~~~r~a~~~L~~~~~v~KLF~~lap 82 (160)
+++||||+++||++|||||+||||+||||+||++||||+|+|||+|||+||+|++|++|+|.++|.|+++++|||++|+|
T Consensus 18 ~~rKLgR~ssHR~AlLRNLvtsLI~hERIeTTlaKAKELR~~AEKLITlAKk~tl~sRR~a~s~L~d~~av~KLF~eLAP 97 (253)
T PTZ00076 18 LFRRAHGQPHHRWDSIKNQLDELLRYGRLELTLPRAKELQQYAEELIYLAKKDTPESNLKVESMLRTPQGRRKLYEKYVP 97 (253)
T ss_pred ccCCCCCCHHHHHHHHHHHHHHHHHcCcEEecHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCHHHHHHHHHHhhh
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhCCCCCCeeEEEcc-cCCCCCCCCeeeeEeccCchhhhcCCCCCCCCC
Q 031427 83 RYKDRAGGYTRLLRS-RIRVGDAAPMAYIEFVDRENELRQSKPAVPQPP 130 (160)
Q Consensus 83 Ry~~R~GGYTRI~kl-~~R~GD~ApmaiIElVd~~~e~~~~~~~~~~~~ 130 (160)
||++|+||||||+|+ ++|.||+||||||||||++.++++++||+.+-.
T Consensus 98 RY~dR~GGYTRIlK~~g~R~GD~ApMAiIELVd~p~e~r~A~pvg~d~~ 146 (253)
T PTZ00076 98 LYRDRPFFFTRVVNQWRLRLRDAAPMAYIEFVDRPGEIRPAKPVGFDKI 146 (253)
T ss_pred HhcCCCCCeeEEEeCCCCCCCCCCCEEEEEeccCcCccccccccchhHH
Confidence 999999999999997 699999999999999999999999999986653
No 5
>KOG3280 consensus Mitochondrial/chloroplast ribosomal protein L17 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.9e-51 Score=327.77 Aligned_cols=150 Identities=53% Similarity=0.796 Sum_probs=142.5
Q ss_pred cCCCCCchHHHHHHHHHHHHHHhccceeecHHhHHHHHhhHHHHHHhh-ccCChHHH--HHHHHhccChhHHHHHHHHHH
Q 031427 5 RKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLG-KEGSLCAA--RRAAAFVRGDDVIHKLFTELA 81 (160)
Q Consensus 5 rklgr~~~hR~allRnlvtsLi~herI~TT~~KAKelr~~aEkLIt~A-K~g~~~~~--r~a~~~L~~~~~v~KLF~~la 81 (160)
+|+||++.||.+|||||||+||+||||+|||+||||+|+|||+|||+| |.|++|.+ +++.+||..+++++|||++||
T Consensus 15 ~Klgr~~~~R~~lLR~lvt~LvkHErIe~t~ara~Ear~~aEklIt~~~k~g~~~~~~~~~a~~~l~ekdli~KlF~vl~ 94 (171)
T KOG3280|consen 15 LKLGRPPAHRLALLRNLVTQLVKHERIETTWARAKEARRYAEKLITLGKKAGSLHERTARMADGWLREKDLLHKLFTVLA 94 (171)
T ss_pred hhcCCCcHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhcCcHhHHHHHHHhcccccchHHHHHHHHhc
Confidence 499999999999999999999999999999999999999999999999 78999987 999999999999999999999
Q ss_pred HhhCCCCCCeeEEEcccCCCCCCCCeeeeEeccCchhhhcCCCCCCCCCCCCCCCHHHHHHhhhccCCCcCCcCCCc
Q 031427 82 YRYKDRAGGYTRLLRSRIRVGDAAPMAYIEFVDRENELRQSKPAVPQPPPRAALDPWTRSRLTKNFAPPKQEKSSDA 158 (160)
Q Consensus 82 pRy~~R~GGYTRI~kl~~R~GD~ApmaiIElVd~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 158 (160)
|||++|+|||||++|+++|.||+|||||||+++|+ .....+..+++..+|.+|++..|.|+|.+|++|+-.+.
T Consensus 95 pRY~dr~ggYTRllrlppr~~d~apmavlE~~Gn~----~p~~~a~~p~~r~~lh~vll~~l~r~~~~~~~e~l~~~ 167 (171)
T KOG3280|consen 95 PRYKDRNGGYTRLLRLPPRRGDRAPMAVLELVGNP----LPQQAADRPDTRVNLHKVLLFRLLREFRPPKEEKLDDS 167 (171)
T ss_pred hhhccCCCCceehhccCcccccccCceeeeecCCc----cccccCCCchhhhhhHHHHHHHHHHHhccchhhcccCc
Confidence 99999999999999999999999999999999876 45677888999999999999999999999999986553
No 6
>PF01196 Ribosomal_L17: Ribosomal protein L17; InterPro: IPR000456 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 L17 is one of the proteins from the large ribosomal subunit. Bacterial L17 is a protein of 120 to 130 amino-acid residues while yeast YmL8 is twice as large (238 residues). The N-terminal half of YmL8 is colinear with the sequence of L17 from Escherichia coli.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3F1F_R 1VSP_L 3PYV_N 3PYR_N 3PYO_N 1VSA_L 3MS1_N 3F1H_R 3D5B_R 3MRZ_N ....
Probab=100.00 E-value=3.4e-48 Score=287.29 Aligned_cols=97 Identities=54% Similarity=0.881 Sum_probs=95.3
Q ss_pred HHHHHHHHHHhccceeecHHhHHHHHhhHHHHHHhhccCChHHHHHHHHhccChhHHHHHHHHHHHhhCCCCCCeeEEEc
Q 031427 17 MLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAYRYKDRAGGYTRLLR 96 (160)
Q Consensus 17 llRnlvtsLi~herI~TT~~KAKelr~~aEkLIt~AK~g~~~~~r~a~~~L~~~~~v~KLF~~lapRy~~R~GGYTRI~k 96 (160)
|||||+|+||+||||+||++||||+|+|||+|||+||+|+.|++|++.+||.|+++++|||++|+|||++|+||||||+|
T Consensus 1 llrnlvt~Li~herI~TT~~KAke~r~~aErlIt~ak~~~~~~~r~~~~~l~~~~~v~KLf~~l~pRy~~r~GgYTRi~k 80 (97)
T PF01196_consen 1 LLRNLVTSLIRHERIETTLAKAKELRPYAERLITLAKKGDLHARRQALSWLRDKELVKKLFKELAPRYADRNGGYTRIIK 80 (97)
T ss_dssp HHHHHHHHHHHHSEEEEEHHHHHHHHHHHHHHHHHHTSSTHHHHHHHHHCSSSHHHHHHHHTTHHHHTTTSSS-SEEEEE
T ss_pred ChHHHHHHHHhCCeEEecHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHhcchHHHHHHHHHHHHHHccCCCCeEEEEe
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCCCeeeeEec
Q 031427 97 SRIRVGDAAPMAYIEFV 113 (160)
Q Consensus 97 l~~R~GD~ApmaiIElV 113 (160)
+++|.||+|||||||||
T Consensus 81 l~~R~gD~A~maiiElV 97 (97)
T PF01196_consen 81 LGPRRGDAAPMAIIELV 97 (97)
T ss_dssp EEECSSSTCEEEEEEET
T ss_pred CCCCCCCCCCEEEEEeC
Confidence 99999999999999998
No 7
>PRK13266 Thf1-like protein; Reviewed
Probab=45.80 E-value=35 Score=29.17 Aligned_cols=78 Identities=19% Similarity=0.279 Sum_probs=60.2
Q ss_pred CCchHHHHHHHHHHHHHHhccceeecHHhHHHHHhhHHHHHHhhccCChHHHHHHHHhccCh--hHHHHHHHHHHHhhCC
Q 031427 9 RPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGD--DVIHKLFTELAYRYKD 86 (160)
Q Consensus 9 r~~~hR~allRnlvtsLi~herI~TT~~KAKelr~~aEkLIt~AK~g~~~~~r~a~~~L~~~--~~v~KLF~~lapRy~~ 86 (160)
++.+|+..++..+|.++= --+.++|..|++|..+|+..+.. .+.+||... .....|...+...=.+
T Consensus 68 ~Pee~~~~IF~Alc~a~~---------~dp~~~r~dA~~l~~~a~~~s~~---~i~~~l~~~~~~~~~~l~~~l~~ia~~ 135 (225)
T PRK13266 68 RPEEHKDSIFNALCQAVG---------FDPEQLRQDAERLLELAKGKSLK---EILSWLTQKALGEPGGLLATLLAIANN 135 (225)
T ss_pred CChHHHHHHHHHHHHHcC---------CCHHHHHHHHHHHHHHHhcCCHH---HHHHHHhccccccchhHHHHHHHHhcC
Confidence 578899999999999863 45889999999999999977654 455677643 2333366777766678
Q ss_pred CCCCeeEEEccc
Q 031427 87 RAGGYTRLLRSR 98 (160)
Q Consensus 87 R~GGYTRI~kl~ 98 (160)
.+--|.|++=+|
T Consensus 136 ~~f~YSRl~AIG 147 (225)
T PRK13266 136 SKFKYSRLFAIG 147 (225)
T ss_pred CCCchHHHHHHH
Confidence 888999998877
No 8
>COG1775 HgdB Benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase subunit, BcrC/BadD/HgdB [Amino acid transport and metabolism]
Probab=42.61 E-value=49 Score=30.47 Aligned_cols=89 Identities=25% Similarity=0.353 Sum_probs=60.6
Q ss_pred HhccceeecHHhHHHHHhhHHHHHHhhccC------ChHHHHHHHH-hccChhHHHHHHHHHHHhhCCC--CCCeeEEEc
Q 031427 26 VKHERIETTVAKAKEVRRLADNMVQLGKEG------SLCAARRAAA-FVRGDDVIHKLFTELAYRYKDR--AGGYTRLLR 96 (160)
Q Consensus 26 i~herI~TT~~KAKelr~~aEkLIt~AK~g------~~~~~r~a~~-~L~~~~~v~KLF~~lapRy~~R--~GGYTRI~k 96 (160)
|..+..+-+.++.-++|..--+++.+++.. ..+...++.+ +++|++...-.++++..+++.| .|+=+||+-
T Consensus 160 iT~e~L~da~~r~N~~rea~~k~~kL~~~~P~plsg~D~~~~~~~~~~~~d~d~~~~~l~~l~eelekr~~eg~~~Ri~~ 239 (379)
T COG1775 160 ITEEKLRDAIARYNRLREALAKLYKLAKHKPSPLSGSDAFNVMAFAVFLRDKDAFIEELEELIEELEKRVEEGEGPRILI 239 (379)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhHHHHHhhHHHHhcchHHHHHHHHHHHHHHHHHHhccCCceEEe
Confidence 345566777888888888888899999753 3455556666 8888887777777766666544 233399999
Q ss_pred ccCC-CCCCCCe-eeeEecc
Q 031427 97 SRIR-VGDAAPM-AYIEFVD 114 (160)
Q Consensus 97 l~~R-~GD~Apm-aiIElVd 114 (160)
.|.| .+|+-+. -++|.+.
T Consensus 240 ~g~p~~~~~~~v~~~~e~~~ 259 (379)
T COG1775 240 TGIPILGDNPKVWEILEEVG 259 (379)
T ss_pred ecCcccCCCcchhHHHHhhc
Confidence 9988 5576653 2445444
No 9
>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=38.58 E-value=69 Score=22.03 Aligned_cols=47 Identities=17% Similarity=0.317 Sum_probs=31.9
Q ss_pred HHHHHhhccCC---hHHHHHHHHhccChhHHHHHHHHHHHh-----hCCCCCCee
Q 031427 46 DNMVQLGKEGS---LCAARRAAAFVRGDDVIHKLFTELAYR-----YKDRAGGYT 92 (160)
Q Consensus 46 EkLIt~AK~g~---~~~~r~a~~~L~~~~~v~KLF~~lapR-----y~~R~GGYT 92 (160)
.=|+.+|..++ ......|...=.++..+.++++.|... ...++|||.
T Consensus 12 ~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy~ 66 (83)
T PF02082_consen 12 RILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGYR 66 (83)
T ss_dssp HHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEEE
T ss_pred HHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCcee
Confidence 34566776654 456677777777888999999998762 355667774
No 10
>PRK13848 conjugal transfer protein TraC; Provisional
Probab=36.40 E-value=36 Score=25.71 Aligned_cols=24 Identities=29% Similarity=0.494 Sum_probs=20.2
Q ss_pred ChhHHHHHHHHHHHhhCCCCCCee
Q 031427 69 GDDVIHKLFTELAYRYKDRAGGYT 92 (160)
Q Consensus 69 ~~~~v~KLF~~lapRy~~R~GGYT 92 (160)
++.-+...|++|+-||.+..|+-|
T Consensus 45 ~d~eL~~aFeeiAaRFR~g~~~~~ 68 (98)
T PRK13848 45 EEAELQAAFEELAKRFRGGKGAAT 68 (98)
T ss_pred CHHHHHHHHHHHHHHHhcCCCccc
Confidence 556789999999999999888654
No 11
>PF05848 CtsR: Firmicute transcriptional repressor of class III stress genes (CtsR); InterPro: IPR008463 This family consists of several Firmicute transcriptional repressor of class III stress gene (CtsR) proteins. CtsR of Listeria monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon [].; PDB: 3H0D_A.
Probab=32.46 E-value=5.2 Score=32.23 Aligned_cols=71 Identities=20% Similarity=0.313 Sum_probs=37.3
Q ss_pred hhHHHHHHhhccCChH--HHHHHHHhccChhHHHHHHHHHHHhhCCC----------CCCeeEEEcccCCCCCCCCeeee
Q 031427 43 RLADNMVQLGKEGSLC--AARRAAAFVRGDDVIHKLFTELAYRYKDR----------AGGYTRLLRSRIRVGDAAPMAYI 110 (160)
Q Consensus 43 ~~aEkLIt~AK~g~~~--~~r~a~~~L~~~~~v~KLF~~lapRy~~R----------~GGYTRI~kl~~R~GD~ApmaiI 110 (160)
.|.-+++..+..|.+. -...|..|=.-|.-+.-+ |.-||..- -|||-||.|+.....+.--..++
T Consensus 10 ~yik~lL~~s~~~~ieIqR~eLA~~F~CvPSQINYV---l~TRFT~e~GY~VESrRGGGGyIRI~rv~~~~~~~~~~~l~ 86 (152)
T PF05848_consen 10 QYIKQLLEESEEGQIEIQRNELAERFNCVPSQINYV---LSTRFTPERGYIVESRRGGGGYIRIVRVPLDDEEDLLDHLI 86 (152)
T ss_dssp HHHHHHHCTSTTSEEEE-HHHHHHHTTS-THHHHHH---HHHHSSCCCTEEEEEE-STT-EEEEEEEEESTCHHHHHHHH
T ss_pred HHHHHHHHhCCCCeEEEeHHHHHHHhCCchhhhhee---eeccccCCCCeEEEeccCCCceEEEEEEccCCcHHHHHHHH
Confidence 3444444444444432 223444454455555543 44588643 57999999987665444445566
Q ss_pred EeccCc
Q 031427 111 EFVDRE 116 (160)
Q Consensus 111 ElVd~~ 116 (160)
+.|++.
T Consensus 87 ~~ig~~ 92 (152)
T PF05848_consen 87 ESIGDS 92 (152)
T ss_dssp CCS-S-
T ss_pred HHhcCc
Confidence 666554
No 12
>PLN00047 photosystem II biogenesis protein Psb29; Provisional
Probab=27.44 E-value=1.3e+02 Score=26.73 Aligned_cols=78 Identities=13% Similarity=0.226 Sum_probs=61.1
Q ss_pred CCchHHHHHHHHHHHHHHhccceeecHHhHHHHHhhHHHHHHhhccCChHHHHHHHHhccChhHHHHHHHHHHHhhC-CC
Q 031427 9 RPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAYRYK-DR 87 (160)
Q Consensus 9 r~~~hR~allRnlvtsLi~herI~TT~~KAKelr~~aEkLIt~AK~g~~~~~r~a~~~L~~~~~v~KLF~~lapRy~-~R 87 (160)
++.+|+..++..+|.++=. -+.++|..|++|..+|+..+.. .+..|+.....+...+..|+.+=. +.
T Consensus 119 ~Pee~~~~IF~Alc~a~g~---------Dp~qyr~dA~~l~~~A~~~s~~---~l~~~l~~~~~l~~~l~~IA~~a~~~~ 186 (283)
T PLN00047 119 PSDEDRDAIFKAYIKALGE---------DPEQYRKDAAKLEEWARSQTGS---SLVDFSSKEGEIEGILKDIAERAGSKG 186 (283)
T ss_pred CChHHHHHHHHHHHHHcCC---------CHHHHHHHHHHHHHHHhcCCHH---HHHHHHhcchHHHHHHHHHHHhhccCC
Confidence 4678999999999998743 5789999999999999976554 455777777778888888886543 35
Q ss_pred CCCeeEEEccc
Q 031427 88 AGGYTRLLRSR 98 (160)
Q Consensus 88 ~GGYTRI~kl~ 98 (160)
.--|.|++=+|
T Consensus 187 ~f~YSRlfAIG 197 (283)
T PLN00047 187 KFSYSRFFAIG 197 (283)
T ss_pred CcchHHHHHHH
Confidence 55799998776
No 13
>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=26.37 E-value=45 Score=29.26 Aligned_cols=46 Identities=20% Similarity=0.311 Sum_probs=31.0
Q ss_pred EeccCchhhhcCCCCCCCCCCCCCCC---HHHHHHh-----hhccCCCcCCcCC
Q 031427 111 EFVDRENELRQSKPAVPQPPPRAALD---PWTRSRL-----TKNFAPPKQEKSS 156 (160)
Q Consensus 111 ElVd~~~e~~~~~~~~~~~~~~~~~~---~~~~~~~-----~~~~~~~~~~~~~ 156 (160)
||.+.-...-.++|+..-+-...|+| +|++++- ..++-++|-+.+|
T Consensus 76 EL~GrtirVN~AkP~kikegsqkPvWADDdWlkk~~g~~q~E~e~eaeK~et~s 129 (298)
T KOG0111|consen 76 ELFGRTIRVNLAKPEKIKEGSQKPVWADDDWLKKQQGEAQAEKEIEAEKAETES 129 (298)
T ss_pred hhcceeEEEeecCCccccCCCCCCcccCcHHHHHhccccccccccchhhhcCcc
Confidence 44444445556889988888888988 8999987 3345555655444
No 14
>PF05598 DUF772: Transposase domain (DUF772); InterPro: IPR008490 This presumed domain is found at the N terminus of transposase insH and other related transposases.
Probab=25.28 E-value=2.1e+02 Score=18.94 Aligned_cols=72 Identities=17% Similarity=0.200 Sum_probs=36.5
Q ss_pred CCCchHHHHHHHHHHHHHHhccceeecHHhHHHHHhhHH--HHHHhhccCCh---HHHHHHHHhccChhHHHHHHHHHH
Q 031427 8 NRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLAD--NMVQLGKEGSL---CAARRAAAFVRGDDVIHKLFTELA 81 (160)
Q Consensus 8 gr~~~hR~allRnlvtsLi~herI~TT~~KAKelr~~aE--kLIt~AK~g~~---~~~r~a~~~L~~~~~v~KLF~~la 81 (160)
||++-+-..|++-++-+-...- .|.-.=...++--.. .+.-+.-.+.. .+-......+.++++.++||+.++
T Consensus 1 GRp~~~~~~ml~~ll~~~~~~~--~S~r~l~~~l~~~~~~r~~~g~~~~~~~pd~stl~rfr~rl~~~~~~~~lf~~~v 77 (77)
T PF05598_consen 1 GRPAYPPRMMLKALLLKYLFGL--RSDRELEERLRDNLSFRYFCGLSLEEPVPDHSTLSRFRKRLIQHGLIEKLFDQVV 77 (77)
T ss_pred CcCCCCHHHHHHHHHHHHHHhc--chHHHHHhhHhhhhHHHHHHhcccCCCCCChHHHHHHHHHHhhccHHHHHHHHhC
Confidence 7777788888888887766532 222111111111111 11111011222 222333356777789999999874
No 15
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=24.78 E-value=1.5e+02 Score=23.60 Aligned_cols=46 Identities=15% Similarity=0.305 Sum_probs=29.4
Q ss_pred HHHHHHhhccCChHHHHHHHHhccChhHHHHHHHHHHHhhCCCCCCee
Q 031427 45 ADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAYRYKDRAGGYT 92 (160)
Q Consensus 45 aEkLIt~AK~g~~~~~r~a~~~L~~~~~v~KLF~~lapRy~~R~GGYT 92 (160)
+|-++..+-.. +. .......+.+.+.+.++.++|..+|.+.++|+.
T Consensus 3 iEAlLF~s~~p-vs-~~~La~~l~~~~~v~~~l~~L~~~y~~~~~gl~ 48 (159)
T PF04079_consen 3 IEALLFASGEP-VS-IEELAEILGSEDEVEEALEELQEEYNEEDRGLE 48 (159)
T ss_dssp HHHHHHH-SS--B--HHHHHHHCT-HHHHHHHHHHHHHHHHHCT-SEE
T ss_pred hHhhHHHcCCC-CC-HHHHHHHhCCHHHHHHHHHHHHHHhccCCCCEE
Confidence 56666666544 33 333344444889999999999999987777764
No 16
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=24.66 E-value=2.2e+02 Score=23.35 Aligned_cols=51 Identities=16% Similarity=0.287 Sum_probs=33.8
Q ss_pred HHhhHHHHHHhhccCChHHHHHHHHhccChhHHHHHHHHHHHhhCCCCCCe
Q 031427 41 VRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAYRYKDRAGGY 91 (160)
Q Consensus 41 lr~~aEkLIt~AK~g~~~~~r~a~~~L~~~~~v~KLF~~lapRy~~R~GGY 91 (160)
+...+|-++..+....+...+.+.-+=.+...|..+.++|...|.+++.|+
T Consensus 5 ~~~~iEA~LF~sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~~gi 55 (188)
T PRK00135 5 YKSIIEALLFVSGEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDDRGL 55 (188)
T ss_pred HHHHHHHHHHHcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCCCE
Confidence 456688888887664233333333222345679999999999999776554
No 17
>COG4463 CtsR Transcriptional repressor of class III stress genes [Transcription]
Probab=22.84 E-value=49 Score=26.83 Aligned_cols=13 Identities=31% Similarity=0.830 Sum_probs=11.0
Q ss_pred CCCeeEEEcccCC
Q 031427 88 AGGYTRLLRSRIR 100 (160)
Q Consensus 88 ~GGYTRI~kl~~R 100 (160)
-|||-||.|..++
T Consensus 64 GGGYIRI~Kv~~~ 76 (153)
T COG4463 64 GGGYIRIIKVEYS 76 (153)
T ss_pred CCceEEEEEeccc
Confidence 5899999998764
No 18
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=20.97 E-value=1.2e+02 Score=18.92 Aligned_cols=21 Identities=5% Similarity=0.224 Sum_probs=17.6
Q ss_pred CCCchHHHHHHHHHHHHHHhc
Q 031427 8 NRPTGHRMSMLRTMVSQLVKH 28 (160)
Q Consensus 8 gr~~~hR~allRnlvtsLi~h 28 (160)
||+.+++.+|.+.+..+|.++
T Consensus 10 grt~eqk~~l~~~i~~~l~~~ 30 (58)
T cd00491 10 GRTDEQKRELIERVTEAVSEI 30 (58)
T ss_pred CCCHHHHHHHHHHHHHHHHHH
Confidence 788889999999888888764
No 19
>COG2257 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]
Probab=20.88 E-value=83 Score=23.58 Aligned_cols=42 Identities=17% Similarity=0.376 Sum_probs=25.3
Q ss_pred hhHHHHHHhhccCChHH---HHHHHHhcc---ChhHHHHHHHHHHHhh
Q 031427 43 RLADNMVQLGKEGSLCA---ARRAAAFVR---GDDVIHKLFTELAYRY 84 (160)
Q Consensus 43 ~~aEkLIt~AK~g~~~~---~r~a~~~L~---~~~~v~KLF~~lapRy 84 (160)
..||++|..||+..++- ..++...+. +..+=..||++++.-|
T Consensus 32 ~iAe~II~~Ake~~Vpi~edp~Lv~~L~~lelg~~IPeelY~vVAEif 79 (92)
T COG2257 32 EIAEKIIEKAKEHGVPIQEDPLLVELLLKLELGDEIPEELYEVVAEIF 79 (92)
T ss_pred HHHHHHHHHHHHcCCCcccCHHHHHHHHhccccccCCHHHHHHHHHHH
Confidence 47999999999987642 223322222 4445556666666544
No 20
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=20.21 E-value=1.3e+02 Score=27.75 Aligned_cols=40 Identities=25% Similarity=0.316 Sum_probs=30.2
Q ss_pred HHHHHhhHHHHHH-hhccCChHHHHHHHHhccChhHHHHHH
Q 031427 38 AKEVRRLADNMVQ-LGKEGSLCAARRAAAFVRGDDVIHKLF 77 (160)
Q Consensus 38 AKelr~~aEkLIt-~AK~g~~~~~r~a~~~L~~~~~v~KLF 77 (160)
.||+|-|.||+|+ ++-..+.+.+.-|+.-|+++.-++.|.
T Consensus 192 sKELq~YF~kvisal~dEs~~~~r~aAl~sLr~dsGlhQLv 232 (450)
T COG5095 192 SKELQMYFDKVISALLDESDEQTRDAALESLRNDSGLHQLV 232 (450)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCccHHHHH
Confidence 5899999999995 666667777777888888765544443
No 21
>PF07820 TraC: TraC-like protein; InterPro: IPR012930 The members of this family are sequences that are similar to TraC (Q84HT8 from SWISSPROT) from Rhizobium etli. The gene encoding this protein is one of a group of genes found on plasmid p42a of Rhizobium etli (strain CFN 42/ATCC 51251) that are thought to be involved in the process of plasmid self-transmission. Mobilisation of plasmid p42a is of importance as it is required for transfer of plasmid p42d, the symbiotic plasmid which carries most of the genes required for nodulation and nitrogen fixation by this symbiotic bacterium. The predicted protein products of p42a are similar to known transfer proteins of Agrobacterium tumefaciens plasmid pTiC58 []. ; GO: 0000746 conjugation
Probab=20.02 E-value=99 Score=23.15 Aligned_cols=21 Identities=24% Similarity=0.466 Sum_probs=17.7
Q ss_pred ChhHHHHHHHHHHHhhCCCCC
Q 031427 69 GDDVIHKLFTELAYRYKDRAG 89 (160)
Q Consensus 69 ~~~~v~KLF~~lapRy~~R~G 89 (160)
+.+-+.+.|++|+.||....+
T Consensus 44 ~d~eL~~~FeeIa~RFrk~~~ 64 (92)
T PF07820_consen 44 SDAELQAAFEEIAARFRKGKK 64 (92)
T ss_pred CHHHHHHHHHHHHHHHhcccc
Confidence 567899999999999987644
Done!